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<h3>
Alexandre Mestiashvili 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/edae9ad5b574172b4b02f4560e3aad2b853c5e58">edae9ad5</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2019-12-06T19:31:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/patches/2to3.patch, use importlib instead of deprecated imp module
</pre>
</li>
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<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/3a2df740db19427511aa5380e94e56abffdfb3d6">3a2df740</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2019-12-06T20:16:05Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch silencing TBB deprecation warnings
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/ddf99c60e805ad0f668f4e5e961840914b189570">ddf99c60</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2019-12-06T20:52:38Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: bump Policy to 4.4.1, add Rules-requires-root: no
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/88e9eb282622223cb71dbe13df8fcbc472093a20">88e9eb28</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2019-12-06T21:40:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
Gbp-Dch: Ignore
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#6d045d7de2b59ac92f2613f1fbd8b3fca3af7e2c">
<span class="new-file">
+
debian/patches/silence_tbb_deprecation_warning.patch
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</a>
</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/ea7fa13e8815cc911840992817d7740e3b6d873e...88e9eb282622223cb71dbe13df8fcbc472093a20#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie2 (2.3.5.1-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Added ref to conda</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * SEQwiki is deprecated</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * d/u/metadata: yamllint</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"> [ Alexandre Mestiashvili ]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Update d/patches/2to3.patch, use importlib instead of deprecated imp module</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Add patch silencing TBB deprecation warnings</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * d/control: bump Policy to 4.4.1, add Rules-requires-root: no</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org> Fri, 06 Dec 2019 22:38:21 +0100</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">bowtie2 (2.3.5.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/ea7fa13e8815cc911840992817d7740e3b6d873e...88e9eb282622223cb71dbe13df8fcbc472093a20#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">@@ -13,7 +13,8 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libclone-perl,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libfile-which-perl,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Rules-requires-root: no</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bowtie2</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bowtie2.git</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Homepage: http://bowtie-bio.sourceforge.net/bowtie2</span>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/ea7fa13e8815cc911840992817d7740e3b6d873e...88e9eb282622223cb71dbe13df8fcbc472093a20#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</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">@@ -5,7 +5,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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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><span class="idiff left right"> bowtie2.bat:</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></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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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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><span class="idiff left right"> import struct</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -15,7 +15,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> def loadBowtieSa(fh):</span>
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32
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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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33
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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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,7 +36,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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36
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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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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> def loadBowtieSaFilename(fn):</span>
</pre>
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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>
</pre>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span><span class="idiff left right"> if __name__ == "__main__":</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span></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>
</pre>
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41
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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>
</pre>
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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">@@ -45,7 +45,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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45
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45
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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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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> assert sa1 != sa2</span>
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47
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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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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="p">@@ -76,4 +76,4 @@</span><span class="idiff left right"> if __name__ == "__main__":</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -76,4 +76,4 @@</span></span>
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49
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49
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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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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> </span>
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51
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> go()</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">@@ -54,7 +54,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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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><span class="idiff left right"> They use the Python infrastructure in th</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></span>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> </span>
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59
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> From root:</span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> </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">@@ -63,7 +63,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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63
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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"> Val Antonescu originally set these up.</span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> </span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="p">@@ -27,7 +27,7 @@</span><span class="idiff left right"> Builds an index consisting of both human</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -27,7 +27,7 @@</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> </span>
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68
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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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,7 +80,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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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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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span><span class="idiff left right"> class Benchmarks(object):</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"> self.set_idx = 0</span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"> return self</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> </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">@@ -89,7 +89,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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89
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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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90
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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><span class="idiff left right"> class TestAccuracy(Runable):</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="p">@@ -250,7 +250,7 @@</span></span>
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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="diff"> delta = [0, 1]</span>
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94
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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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95
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> try:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,7 +114,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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114
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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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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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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="p">@@ -49,7 +49,7 @@</span><span class="idiff left right"> class SamHeader(object):</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="p">@@ -49,7 +49,7 @@</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"> self.curr_idx = 0</span>
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119
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119
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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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -123,7 +123,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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123
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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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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="diff"> raise StopIteration</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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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="p">@@ -114,7 +114,7 @@</span><span class="idiff left right"> class SamReader(object):</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="p">@@ -114,7 +114,7 @@</span></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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -148,7 +148,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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148
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="diff"> """</span>
</pre>
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149
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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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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span><span class="idiff left right"> Note: This would look so much better rep</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="p">@@ -6,7 +6,7 @@</span></span>
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152
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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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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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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="diff"> import gzip</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">@@ -157,7 +157,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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157
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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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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="diff"> </span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="p">@@ -66,14 +66,14 @@</span><span class="idiff left right"> class LargeTestsData(object):</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="p">@@ -66,14 +66,14 @@</span></span>
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161
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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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -174,7 +174,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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174
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174
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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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175
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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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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><span class="idiff left right"> class LargeTestsData(object):</span></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></span>
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178
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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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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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -204,7 +204,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="diff"> import inspect</span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="diff"> import unittest</span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="diff"> import logging</span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"><span class="p">@@ -69,7 +69,7 @@</span><span class="idiff left right"> class TestLargeIndex(unittest.TestCase):</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="p">@@ -69,7 +69,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="diff"> </span>
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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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -237,3 +237,12 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200</td>
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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>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import imp</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import importlib</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> import inspect</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> import logging</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/bowtie2/compare/ea7fa13e8815cc911840992817d7740e3b6d873e...88e9eb282622223cb71dbe13df8fcbc472093a20#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,3 +5,4 @@ reproducible.patch</td>
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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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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">2to3.patch</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">silence_tbb_deprecation_warning.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/compare/ea7fa13e8815cc911840992817d7740e3b6d873e...88e9eb282622223cb71dbe13df8fcbc472093a20#6d045d7de2b59ac92f2613f1fbd8b3fca3af7e2c"><strong>debian/patches/silence_tbb_deprecation_warning.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Subject: Silence TBB deprecation warnings, including specific headers only</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Alex Mestiashvili <amestia@rsh2.donotuse.de></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/bt2_search.h</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/bt2_search.h</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -21,7 +21,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> #define BT2_SEARCH_H_</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #ifdef WITH_TBB</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <tbb/tbb.h></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> #include <tbb/task_group.h></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"> class multiseedSearchWorker {</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/blockwise_sa.h</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/blockwise_sa.h</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -21,7 +21,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> #define BLOCKWISE_SA_H_</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #ifdef WITH_TBB</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <tbb/tbb.h></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> #include <tbb/task_group.h></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bowtie2.orig/diff_sample.h</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bowtie2/diff_sample.h</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -21,7 +21,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> #define DIFF_SAMPLE_H_</span>
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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"> #ifdef WITH_TBB</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;">-#include <tbb/tbb.h></span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> #include <tbb/task_group.h></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span></pre>
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