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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pysam">Debian Med / python-pysam</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/6b346cfebf668e28e6d94c80853d5d3214a753fb">6b346cfe</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-06T17:44:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make the build reproducible
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/f63e502930995b48effc991358e1ef87ed9a37de">f63e5029</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-06T17:44:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/7483b5c2d6dce62ac1dd188cb83364142ab06d89">7483b5c2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-06T17:44:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/copyright: use spaces rather than tabs to start continuation lines.
Fixes lintian: tab-in-licence-text
See https://lintian.debian.org/tags/tab-in-licence-text.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/a6a8463f5fdd130b194a72c325bb24769a410925">a6a8463f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-06T17:44:22+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/9f8aea852ea0382c141675f28300d87256c562ff">9f8aea85</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-06T17:55:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
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</li>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-pysam/compare/5b7040fc8921a49f8f6c47d4f3235b8b2359e301...9f8aea852ea0382c141675f28300d87256c562ff#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pysam (0.15.3+ds-5) 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"> [ Chris Lamb ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * make the build reproducible</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #948280</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * debian/copyright: use spaces rather than tabs to start continuation</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> lines.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Repository, Repository-</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Browse.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 06 Jan 2020 17:44:23 +0100</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">python-pysam (0.15.3+ds-4) unstable; urgency=medium</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"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-pysam/compare/5b7040fc8921a49f8f6c47d4f3235b8b2359e301...9f8aea852ea0382c141675f28300d87256c562ff#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">@@ -21,7 +21,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> bcftools (>= 1.9) <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> python-pytest <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> python3-pytest <!nocheck></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-pysam</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Homepage: https://pysam.readthedocs.org/en/latest</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">@@ -6,26 +6,26 @@ Files-Excluded: htslib/*</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Copyright: 2009-2018 Andreas Heger,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Tildon Grant Belgrad,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Martin Goodson,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Kevin Jacobs <jacobs@bionformed.com></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> 2008-2010 Genome Research Ltd.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"><span class="idiff left right"> </span> Tildon Grant Belgrad,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><span class="idiff left right"> </span> Martin Goodson,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><span class="idiff left right"> </span> Kevin Jacobs <jacobs@bionformed.com></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"><span class="idiff left right"> </span> 2008-2010 Genome Research Ltd.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Files: bcftools/*</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Copyright:</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> 2013-2018 Genome Research Ltd.</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> 2010-2011 Broad Institute</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"><span class="idiff left right"> </span> 2013-2018 Genome Research Ltd.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"><span class="idiff left right"> </span> 2010-2011 Broad Institute</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">License: MIT</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">Files: samtools/*</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Copyright: 2009-2012 Broad Institute</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"><span class="idiff left right"> </span> 2008-2014 Genome Research Ltd.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"><span class="idiff left right"> </span> 2008-2014 Genome Research Ltd.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Files: samtools/bam_cat.*</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Copyright: 2008-2009, 2011-2013 Genome Research Ltd.</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"><span class="idiff left right"> </span> 2010 Illumina, Inc.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"><span class="idiff left right"> </span> 2010 Illumina, Inc.</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Files: samtools/bam_color.*</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">@@ -35,8 +35,8 @@ License: MIT</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Files: samtools/bam_index.*</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> samtools/bam_mate.*</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Copyright: 2008-2014 Genome Research Ltd.</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"><span class="idiff left right"> </span> 2010-2011 Broad Institute</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"><span class="idiff left right"> </span> 2012-2013 Peter Cock, The James Hutton Institute</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"><span class="idiff left right"> </span> 2010-2011 Broad Institute</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"><span class="idiff left right"> </span> 2012-2013 Peter Cock, The James Hutton Institute</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Files: samtools/misc/ace2sam.*</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">@@ -45,8 +45,8 @@ License: MIT</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Files: samtools/padding.*</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Copyright: 2011-2012 Broad Institute</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"><span class="idiff left right"> </span> 2014 Genome Research Ltd.</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"><span class="idiff left right"> </span> 2012-2013 Peter Cock, The James Hutton Institute</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"><span class="idiff left right"> </span> 2014 Genome Research Ltd.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"><span class="idiff left right"> </span> 2012-2013 Peter Cock, The James Hutton Institute</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">Files: win32/stdint.h</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">@@ -59,10 +59,10 @@ License: LGPL-2.1+</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">Copyright:</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> 2015-2016 Afif Elghraoui <afif@debian.org></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> 2015 Jorge Soares <j.s.soares@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> 2014-2015 Charles Plessy <plessy@debian.org></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> 2014-2018 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"><span class="idiff left right"> </span> 2015-2016 Afif Elghraoui <afif@debian.org></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"><span class="idiff left right"> </span> 2015 Jorge Soares <j.s.soares@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"><span class="idiff left right"> </span> 2014-2015 Charles Plessy <plessy@debian.org></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"><span class="idiff left right"> </span> 2014-2018 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">License: BSD-3-clause</span>
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<a href="https://salsa.debian.org/med-team/python-pysam/compare/5b7040fc8921a49f8f6c47d4f3235b8b2359e301...9f8aea852ea0382c141675f28300d87256c562ff#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -54,10 +54,10 @@ pysam_data.%:</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">clean-tests: pysam_data.clean cbcf_data.clean</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> find . -name "*.pyc" -delete</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"> find . -name "*.pyxbldc" -delete</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> <span class="idiff left right">#find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> <span class="idiff left right">find . -name "tmp_*.bam" -delete</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> find . -name "*.bai*" -delete</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> find . -name "*.cram*" -delete</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> <span class="idiff left right">#find . -name "*.bam" -delete # which deletes files tested</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> <span class="idiff left right">find . -name "pysam_uncompressed.bam" -delete</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> rm -rf tests/pysam_test_work \</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> tests/example_htslib.gtf.gz.tbi \</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> tests/log.txt \</span>
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<a href="https://salsa.debian.org/med-team/python-pysam/compare/5b7040fc8921a49f8f6c47d4f3235b8b2359e301...9f8aea852ea0382c141675f28300d87256c562ff#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Registry:</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> - Name: OMICtools</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Entry: OMICS_19073</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> - Name: SciCrunch</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Entry: NA</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> - Name: bio.tools</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Entry: pysam</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Entry: pysam</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Repository: https://github.com/pysam-developers/pysam</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Entry: OMICS_19073</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">- Name: SciCrunch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Entry: NA</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- Name: bio.tools</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Entry: pysam</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">- Name: conda:bioconda</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Entry: pysam</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Repository: https://github.com/pysam-developers/pysam.git</span>
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<td class="diff-line-num new old_line" data-linenumber="11" 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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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Bug-Database: https://github.com/pysam-developers/pysam/issues</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Repository-Browse: https://github.com/pysam-developers/pysam</span></pre>
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