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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/f563928b9f5afa4950db57d8328afb751b13ea87">f563928b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-04T13:21:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/a96c63da908426d3d7d81640e3304eb8be5dfc48">a96c63da</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-09-04T13:22:06Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete fields Name, Contact from debian/upstream/metadata.</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<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
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/2321febd4e3b249d2bb401e654914b8380b703aa...a96c63da908426d3d7d81640e3304eb8be5dfc48#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -2,17 +2,20 @@ bowtie2 (2.3.5.1-1) UNRELEASED; urgency=medium</td>
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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"> * Team upload</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"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * bowtie-examples: set Multi-Arch: foreign</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * Standards-Version: 4.3.0</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version - yet fails to build -> crash</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 24 Dec 2018 04:19:34 -0800</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> Closes: #936233</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Remove obsolete fields Name, Contact from debian/upstream/metadata.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 04 Sep 2019 15:18:29 +0200</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">bowtie2 (2.3.4.3-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/2321febd4e3b249d2bb401e654914b8380b703aa...a96c63da908426d3d7d81640e3304eb8be5dfc48#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/936233</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: Wed, 04 Sep 2019 15:18:29 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/Makefile</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/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -481,11 +481,11 @@</span> bowtie2.bat:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> bowtie2-build.bat:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> echo "@echo off" > bowtie2-build.bat</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;">- echo "python %~dp0/bowtie2-build %*" >> bowtie2-build.bat</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;">+ echo "python3 %~dp0/bowtie2-build %*" >> bowtie2-build.bat</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> bowtie2-inspect.bat:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> echo "@echo off" > bowtie2-inspect.bat</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;">- echo "python %~dp0/bowtie2-inspect %*" >> bowtie2-inspect.bat</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;">+ echo "python3 %~dp0/bowtie2-inspect %*" >> bowtie2-inspect.bat</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> .PHONY: bowtie2-src-pkg</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> bowtie2-src-pkg: $(SRC_PKG_LIST)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/sa.py</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/sa.py</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> sa.py</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -15,7 +15,7 @@</span> import struct</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> def loadBowtieSa(fh):</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> """ Load a .sa file from handle into an array of ints """</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> nsa = struct.unpack('I', fh.read(4))[0]</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return [ struct.unpack('I', fh.read(4))[0] for i in xrange(0, nsa) ]</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return [ struct.unpack('I', fh.read(4))[0] for i in range(0, nsa) ]</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> def loadBowtieSaFilename(fn):</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> """ Load a .sa file from filename into an array of ints """</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span> if __name__ == "__main__":</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> # Suffix array is in sas; note that $ is considered greater than all</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> # other characters</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> if ref is not None:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(1, len(sas)):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(1, len(sas)):</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> sa1, sa2 = sas[i-1], sas[i]</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> assert sa1 != sa2</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> # Sanity check that suffixes are really in order</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -76,4 +76,4 @@</span> if __name__ == "__main__":</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> assert sas[-1] == len(ref)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> go()</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/test/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/test/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span> They use the Python infrastructure in th</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> From root:</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python scripts/test/regressions.py --verbose</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 scripts/test/regressions.py --verbose</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> Val Antonescu originally set these up.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -27,7 +27,7 @@</span> Builds an index consisting of both human</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> From root:</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python scripts/test/large_idx.py --verbose</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 scripts/test/large_idx.py --verbose</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> #### Randomized tests</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/test/benchmark/benchmarks.py</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/test/benchmark/benchmarks.py</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC79" 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="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"> A few items to deal with sets of benchmarks.</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span> class Benchmarks(object):</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> self.set_idx = 0</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> return self</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> </span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def next(self):</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def __next__(self):</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> if self.set_idx == len(self.values):</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> raise StopIteration</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="p">@@ -250,7 +250,7 @@</span> class TestAccuracy(Runable):</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> delta = [0, 1]</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> logging.debug("%s: missed (pos:%d vs %d)" % (q_name, orig[1], rec.pos))</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mapq_summary[rec.mapq] = map(sum, zip(delta, mapq_summary[rec.mapq]))</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mapq_summary[rec.mapq] = list(map(sum, list(zip(delta, mapq_summary[rec.mapq]))))</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> except KeyError:</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> mapq_summary[rec.mapq] = delta</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/test/benchmark/run.py</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/test/benchmark/run.py</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></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"> Runs benchmark sets specified in JSON files.</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> </span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/test/benchmark/samreader.py</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/test/benchmark/samreader.py</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</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;">+#!/usr/bin/python3</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> """</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> A reader of SAM format.</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="p">@@ -49,7 +49,7 @@</span> class SamHeader(object):</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> self.curr_idx = 0</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> return self</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> </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;">- def next(self):</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def __next__(self):</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> if self.curr_idx == len(self.header_lines):</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> raise StopIteration</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="p">@@ -114,7 +114,7 @@</span> class SamReader(object):</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> self._source_fh.seek(self.header.end_header_pointer)</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> return self</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> </span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def next(self):</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def __next__(self):</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> line = self._source_fh.readline()</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> if not line:</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> raise StopIteration</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/test/bt2face.py</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/test/bt2face.py</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</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;">+#!/usr/bin/python3</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"> import os</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> import logging</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/test/btdata.py</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/test/btdata.py</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</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;">+#!/usr/bin/python3</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> """</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> Note: This would look so much better replaced by XML or at least JSON. But </span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> is not worth to do it for now.</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span> Note: This would look so much better rep</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> import os</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> import gzip</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import urllib2</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import urllib.request, urllib.error, urllib.parse</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> import logging</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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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="p">@@ -66,14 +66,14 @@</span> class LargeTestsData(object):</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> def init_data(self):</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> """ Try and init the data we need.</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for genome,gdata in self.genomes.iteritems():</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for genome,gdata in self.genomes.items():</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> gn_path = os.path.join(self.data_dir_path,genome)</span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> gn_fasta = os.path.join(gn_path,gdata['ref_name'])</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> if not os.path.exists(gn_fasta):</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> self._get_genome(genome)</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> self._build_genome(genome)</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for genome,gdata in self.joint_genomes.iteritems():</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for genome,gdata in self.joint_genomes.items():</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> gn_path = os.path.join(self.data_dir_path,genome)</span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> gn_fasta = os.path.join(gn_path,gdata['ref_name'])</span>
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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
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> if not os.path.exists(gn_fasta):</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="p">@@ -103,7 +103,7 @@</span> class LargeTestsData(object):</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> </span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> try:</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> f = open(fname,'wb')</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- u = urllib2.urlopen(uri)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ u = urllib.request.urlopen(uri)</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> f.write(u.read())</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> except:</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> f.close()</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/test/dataface.py</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/test/dataface.py</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</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;">+#!/usr/bin/python3</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> </span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> import os</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> import logging</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/test/large_idx.py</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/test/large_idx.py</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="p">@@ -1,8 +1,8 @@</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></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"> import os</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> import gzip</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import urllib2</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import urllib.request, urllib.error, urllib.parse</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> import inspect</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> import unittest</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> import logging</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="p">@@ -69,7 +69,7 @@</span> class TestLargeIndex(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> </span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> def get_suite():</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> tests = ['test_human','test_mouse','test_large_index']</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return unittest.TestSuite(map(TestLargeIndex,tests))</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return unittest.TestSuite(list(map(TestLargeIndex,tests)))</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/test/regressions.py</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/test/regressions.py</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC220" 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="LC221" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> import inspect</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bowtie2-build</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bowtie2-build</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC227" 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="LC228" 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="LC229" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> Copyright 2014, Ben Langmead <langmea@cs.jhu.edu></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bowtie2-inspect</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bowtie2-inspect</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC235" 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="LC236" 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="LC237" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> Copyright 2014, Ben Langmead <langmea@cs.jhu.edu></span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/2321febd4e3b249d2bb401e654914b8380b703aa...a96c63da908426d3d7d81640e3304eb8be5dfc48#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -4,3 +4,4 @@ hardening.patch</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">reproducible.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">skip_test_requiring_non-free_libmath-random-perl.patch</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="plaintext">do-not-rebuild-during-test.patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/2321febd4e3b249d2bb401e654914b8380b703aa...a96c63da908426d3d7d81640e3304eb8be5dfc48#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Contact: Ben Langmead <blangmea@jhsph.edu></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Name: Bowtie2</span>
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3
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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4
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> Author: Ben Langmead and Steven L Salzberg</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> Title: Fast gapped-read alignment with Bowtie 2</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">@@ -12,11 +10,11 @@ Reference:</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> URL: http://www.nature.com/nmeth/journal/v9/n4/abs/nmeth.1923.html</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> ISSN: 1548-7105</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: SEQwiki</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: Bowtie</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: SciCrunch</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: SCR_005476</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">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: OMICtools</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: OMICS_31633</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: bio.tools</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: bowtie2</span></pre>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">- Name: SEQwiki</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Entry: Bowtie</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- Name: SciCrunch</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Entry: SCR_005476</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">- Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Entry: OMICS_31633</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">- Name: bio.tools</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Entry: bowtie2</span></pre>
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