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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/adapterremoval">Debian Med / adapterremoval</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/adapterremoval/commit/a277e55ebcb954281a6640b48c10244b6517be5f">a277e55e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T14:16:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Convert benchmark scripts from Python2 to Python3 using 2to3 even if not used in package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/adapterremoval/commit/9d2f27707fb22a78039860d6d62287d8bb5ff0a6">9d2f2770</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T14:21:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/adapterremoval/commit/8e8982f91a050eeeabfc0b9ea086ca9050c9bbd3">8e8982f9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T14:21:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/adapterremoval/commit/fdd173563fafb0cd4d8fe6965414cb802123a9d8">fdd17356</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T14:21:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/adapterremoval/commit/bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525">bb4d0b2f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T14:24:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/adapterremoval/compare/66da507481041f1aa19da8222e1af44410f88820...bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">adapterremoval (2.3.1-2) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">adapterremoval (2.3.1-2) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Build-Depends: markdown instead of python-markdown</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 02 Sep 2019 08:59:12 +0200</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #942927</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Convert benchmark scripts from Python2 to Python3 using 2to3 even</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> if not used in package</span>
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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"> * Standards-Version: 4.4.1</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"> * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Repository, Repository-</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Browse.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sun, 15 Dec 2019 15:21:21 +0100</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">adapterremoval (2.3.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/adapterremoval/compare/66da507481041f1aa19da8222e1af44410f88820...bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libgtest-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> markdown</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/adapterremoval</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/adapterremoval.git</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://github.com/MikkelSchubert/adapterremoval</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" 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">@@ -46,7 +46,7 @@ Description: rapid adapter trimming, identification, and read merging (example d</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">#Package: adapter-benchmark</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">#Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">#Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"># python,</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"># python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"># adapterremoval,</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"># cutadapt,</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"># ea-utils,</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/adapterremoval/compare/66da507481041f1aa19da8222e1af44410f88820...bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525#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: Convert benchmark scripts from Python2 to Python3 using 2to3 even if not used in package</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/942927</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: Sun, 15 Dec 2019 15:12:53 +0100</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/benchmark/benchmark.sh</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/benchmark/benchmark.sh</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -194,7 +194,7 @@</span> function shuffle_and_run()</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> echo > /dev/stderr</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> echo "Shuffling batch ..." > /dev/stderr</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </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;">- python -c "import sys, random</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;">+ python3 -c "import sys, random</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> lines = sys.stdin.readlines()</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> random.shuffle(lines)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> sys.stdout.write(''.join(lines))" |</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/benchmark/scripts/evaluate.py</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/benchmark/scripts/evaluate.py</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC21" 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="LC22" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> # Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -131,10 +131,10 @@</span> class Summary(object):</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> def missing_reads(expectations, se_mode):</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> if se_mode:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> reads = [(key, [pair[0], None])</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key, pair in expectations.iteritems()</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key, pair in expectations.items()</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> if pair[0] is not None]</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- reads = [(key, pair) for key, pair in expectations.iteritems()</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ reads = [(key, pair) for key, pair in expectations.items()</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> if pair != [None, None]]</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> max_errors = 0</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -238,7 +238,7 @@</span> def evaluate(args, expectations, trimmed</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> eval_func(args, expectations, stat, record)</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> if args.dimers_are_discarded:</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key, pair in expectations.items():</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key, pair in list(expectations.items()):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> if args.read_mode in ("SE", "MIXED_SE"):</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> pair[1] = None</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -313,7 +313,7 @@</span> def read_expected_lengths(args):</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> results = collections.defaultdict(lambda: [None, None])</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> for line in open_ro(args.read_info):</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> if line.startswith("@"):</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- record = dict(zip(header, line.rstrip().split('\t')))</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ record = dict(list(zip(header, line.rstrip().split('\t'))))</span></span>
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53
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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"> name = record["readId"][1:]</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> name, mate = name.split("/")</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/benchmark/scripts/evaluate_dmux.py</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/benchmark/scripts/evaluate_dmux.py</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> # Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.com></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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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -54,7 +54,7 @@</span> def read_barcodes(filename):</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> results = {}</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> for line in open_ro(filename):</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> if line.startswith("@"):</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- record = dict(zip(header, line.rstrip().split('\t')))</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ record = dict(list(zip(header, line.rstrip().split('\t'))))</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> name = record["readId"].split("/")[0]</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> results[name] = "_".join((record["barcode_1"], record["barcode_2"]))</span>
</pre>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -90,7 +90,7 @@</span> def main(argv):</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> if expectations[name] == barcode:</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> correct += 1</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> else:</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print expectations[name], barcode</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(expectations[name], barcode)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> total += 1</span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> handle.readline()</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -98,7 +98,7 @@</span> def main(argv):</span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> handle.readline()</span>
</pre>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> header = handle.readline()</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print total, correct</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(total, correct)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> return 0</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/benchmark/scripts/evaluate_id.py</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/benchmark/scripts/evaluate_id.py</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> # Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.com></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> #</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="p">@@ -56,7 +56,7 @@</span> class evalulate_minion(object):</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> def __call__(self, readlen, insert_mean, replicate, fpath):</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> prefix = os.path.join(fpath, "mate")</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for method, result in self._parse_report_minion(prefix).items():</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for method, result in list(self._parse_report_minion(prefix).items()):</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> self._results[(readlen, insert_mean, method)][replicate] = result</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> def finalize(self):</span>
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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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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="p">@@ -88,7 +88,7 @@</span> class evalulate_minion(object):</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> results.append(result)</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> result = {}</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> else:</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- key, value = map(str.strip, line.split("=", 1))</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ key, value = list(map(str.strip, line.split("=", 1)))</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> result[key] = value</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> if result:</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="p">@@ -132,13 +132,13 @@</span> class evalulate_adapterrm(object):</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> def print_rows(program, results):</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> rows = []</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> for (readlen, insert_mean, method), replicates in sorted(results.items()):</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mean_pcr1 = numpy.mean([repl["PCR1"] for repl in replicates.values()])</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mean_pcr2 = numpy.mean([repl["PCR2"] for repl in replicates.values()])</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mean_pcr1 = numpy.mean([repl["PCR1"] for repl in list(replicates.values())])</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mean_pcr2 = numpy.mean([repl["PCR2"] for repl in list(replicates.values())])</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> rows.append((method, readlen, insert_mean, mean_pcr1, mean_pcr2))</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> </span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> for row in sorted(rows):</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(map(str, row))</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(map(str, row)))</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> </span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> def main(argv):</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="p">@@ -149,14 +149,14 @@</span> def main(argv):</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> }</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> </span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> for run in os.listdir(args.root):</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- readlen, insert_mean, replicate = map(int, run.split("_"))</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ readlen, insert_mean, replicate = list(map(int, run.split("_")))</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> </span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> for program in os.listdir(os.path.join(args.root, run)):</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> if program in eval_funcs:</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> fpath = os.path.join(args.root, run, program)</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> eval_funcs[program](readlen, insert_mean, replicate, fpath)</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> </span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(("Method", "ReadLen", "InsertMean", "PCR1", "PCR2"))</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(("Method", "ReadLen", "InsertMean", "PCR1", "PCR2")))</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> for program, func in sorted(eval_funcs.items()):</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> print_rows(program, func.finalize())</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> </span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/benchmark/scripts/extend_profile.py</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/benchmark/scripts/extend_profile.py</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> # Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.com></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> #</span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="p">@@ -84,13 +84,13 @@</span> def main(argv):</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> elif not line_s or line_s.startswith("#") or line_s == "<<END":</span>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> if rows:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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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="LC162" class="line" lang="diff"> for row in sorted(rows):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(map(str, row))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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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="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(map(str, row)))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> rows = []</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> in_table = False</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> in_table_header = None</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="169" 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">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- row = dict(zip(in_table_header,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- map(try_cast, line_s.split('\t'))))</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="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ row = dict(list(zip(in_table_header,</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="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ list(map(try_cast, line_s.split('\t'))))))</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="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> row["Cycle"] = row["Cycle"] * 2</span>
</pre>
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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"> rows.append(tuple(row[key] for key in in_table_header))</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="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> row["Cycle"] = row["Cycle"] - 1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
</td>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="p">@@ -99,10 +99,10 @@</span> def main(argv):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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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="LC177" class="line" lang="diff"> elif line.startswith("["):</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="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> in_table = True</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="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" 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="180" 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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print line,</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="181" 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">
181
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(line, end=' ')</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="182" 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">
182
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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="LC182" 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="183" 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">
183
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> for row in sorted(rows):</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="184" 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">
184
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(map(str, row))</span></span>
</pre>
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</tr>
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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="185" 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">
185
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(map(str, row)))</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> </span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> return 0</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/benchmark/scripts/merge_tables.py</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/benchmark/scripts/merge_tables.py</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> # Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.com></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> #</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="p">@@ -58,18 +58,18 @@</span> def main(argv):</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> assert False, fpath</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> </span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> for line in handle:</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rows.append(dict(zip(header, line.rstrip().split('\t'))))</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rows.append(dict(list(zip(header, line.rstrip().split('\t')))))</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> rows[-1]["Nth"] = str(int(replicate)) # Strip leading zeros</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> rows[-1]["ReadLen"] = readlen</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> </span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> keys.insert(0, "Nth")</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> keys.insert(0, "ReadLen")</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(keys)</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(keys))</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> rows = ["\t".join(row.get(key, "NA") for key in keys) for row in rows]</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> rows.sort()</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> </span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> for row in rows:</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print row</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(row)</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> </span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> return 0</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/benchmark/scripts/shuffle_fasta.py</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/benchmark/scripts/shuffle_fasta.py</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC223" 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="LC224" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> # Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="p">@@ -55,15 +55,15 @@</span> def shuffle(rng, seq):</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> def main(argv):</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> args = parse_args(argv)</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> if args.seed is None:</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- args.seed = random.randint(0, sys.maxint)</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ args.seed = random.randint(0, sys.maxsize)</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> rng = random.Random(args.seed)</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> name, sequence = read_fasta(args.file)</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Seed =", args.seed</span></span>
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<td class="diff-line-num new new_line" data-linenumber="237" 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">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Seq =", sequence</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Seed =", args.seed)</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Seq =", sequence)</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> </span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for _ in xrange(args.replicates - 1):</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "New =", shuffle(rng, sequence)</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for _ in range(args.replicates - 1):</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("New =", shuffle(rng, sequence))</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> </span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> return 0</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> </span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/benchmark/scripts/tabulate.py</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/benchmark/scripts/tabulate.py</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" 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="LC253" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> # Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="p">@@ -43,7 +43,7 @@</span> def read_table(fpath, filter_func):</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> for line in handle:</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> fields = line.rstrip().split("\t")</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> assert len(fields) == len(header), (header, fields)</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- row = dict(zip(header, fields))</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ row = dict(list(zip(header, fields)))</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> </span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> name = row["Name"]</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> if name.endswith("_gz") or name.endswith("_bz2"):</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="p">@@ -90,17 +90,17 @@</span> def _collapse_basic(rows):</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> subdd[key_nth] = row</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="269" 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">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key, values in results.iteritems():</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key, values in results.items():</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> assert len(values) == max_nth and max(values) == max_nth, values</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> </span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> collapsed_rows = []</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> value_keys = ("SEN", "SPC", "PPV", "NPV", "MCC", "Rate")</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for rows in results.itervalues():</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for rows in results.values():</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> result = {}</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> </span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> for key in value_keys:</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if any((key in row) for row in rows.itervalues()):</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- values = tuple(float(row[key]) for row in rows.itervalues())</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if any((key in row) for row in rows.values()):</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ values = tuple(float(row[key]) for row in rows.values())</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> result[key] = "%.3f" % (numpy.mean(values),)</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> for key in keys:</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="p">@@ -138,17 +138,17 @@</span> def _collapse_throughput(rows):</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> </span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> subdd[key] = row["Rate"]</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> </span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key, values in results.iteritems():</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key, values in results.items():</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> assert len(values) == max_nth and max(values) == max_nth, values</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> collapsed_rows = []</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> value_keys = tuple(sorted(rate_keys))</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for rows in results.itervalues():</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for rows in results.values():</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> result = {}</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> for key in value_keys:</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if any((key in row) for row in rows.itervalues()):</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- values = tuple(float(row[key]) for row in rows.itervalues())</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if any((key in row) for row in rows.values()):</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ values = tuple(float(row[key]) for row in rows.values())</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> result[key] = "%.1f" % (numpy.mean(values),)</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> for key in keys:</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="p">@@ -193,9 +193,9 @@</span> def main(argv):</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> for row in sorted(rows):</span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> output_rows.append(tuple(str(row.get(key, "NA")) for key in keys))</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> </span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(keys)</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(keys))</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> for row in sorted(output_rows):</span>
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<td class="diff-line-num new new_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\t".join(row)</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\t".join(row))</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> </span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> return 0</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> </span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/adapterremoval/compare/66da507481041f1aa19da8222e1af44410f88820...bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525#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">adapt-benchmarking.patch</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">reduce_benchmark_length.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">delete_adapterremoval1x_completely.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">2to3.patch</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/adapterremoval/compare/66da507481041f1aa19da8222e1af44410f88820...bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -e</span></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="shell"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>adapterremoval</span>
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<td class="diff-line-num old old_line" data-linenumber="4" 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">
4
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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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5
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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">DT</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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<a href="https://salsa.debian.org/med-team/adapterremoval/compare/66da507481041f1aa19da8222e1af44410f88820...bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> Author: Mikkel Schubert and Stinus Lindgreen and Ludovic Orlando</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> AdapterRemoval v2: rapid adapter trimming, identification,</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> and read merging</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right"> </span>AdapterRemoval v2: rapid adapter trimming, identification,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>and read merging</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Journal: BMC Research Notes</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> Year: 2016</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> Volume: 9</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">@@ -10,13 +10,16 @@ Reference:</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> DOI: 10.1186/s13104-016-1900-2</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> PMID: 26868221</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> URL: |</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right"> </span>http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> eprint: |</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> http://bmcresnotes.biomedcentral.com/track/pdf/10.1186/s13104-016-1900-2</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> <span class="idiff left right"> </span>http://bmcresnotes.biomedcentral.com/track/pdf/10.1186/s13104-016-1900-2</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> - Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC18" class="line" lang="plaintext"> Entry: OMICS_01081</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC19" class="line" lang="plaintext"> - Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="20" 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">
20
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC20" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num old old_line" data-linenumber="21" 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">
21
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC21" class="line" lang="plaintext"> - Name: SciCrunch</span>
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<td class="diff-line-num old old_line" data-linenumber="22" 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">
22
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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC22" class="line" lang="plaintext"> Entry: SCR_011834</span></pre>
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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">- Name: OMICtools</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Entry: OMICS_01081</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">- Name: bio.tools</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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="20" 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">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Entry: NA</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">- Name: SciCrunch</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Entry: SCR_011834</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Bug-Database: https://github.com/MikkelSchubert/adapterremoval/issues</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Repository: https://github.com/MikkelSchubert/adapterremoval.git</span>
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<td class="diff-line-num new old_line" data-linenumber="23" 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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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Repository-Browse: https://github.com/MikkelSchubert/adapterremoval</span></pre>
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