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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/samtools">Debian Med / samtools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/commit/0b80afbb6a271787c6646227e81e2319e6127cf3">0b80afbb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-03T10:45:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Port Python2 script to Python3 using 2to3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/commit/30c291791df4584a21a2a8805bffeeceba3da926">30c29179</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-03T10:45:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/commit/909aa9ba67a535c60342197893b9e1e6fd7b7ae3">909aa9ba</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-03T10:45:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set fields Upstream-Name in debian/copyright.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/commit/8bf7ff1d4ac22e464b12cdbabf459a1c889804b5">8bf7ff1d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-03T10:45:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/commit/82f11d9cac7a15c24bb02b9336e92bc5a8412cc7">82f11d9c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-03T10:45:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete fields Name from debian/upstream/metadata.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/commit/0a09a539872c8501664903b5e9d868bd29635eed">0a09a539</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-03T10:50:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use python3 dependency once the script was converted
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/samtools/commit/49f62d75292e384dc9f7a85d72a27c9ffba030d6">49f62d75</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-03T10:55:41Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
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<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/samtools/compare/5b1c474ae5873ebf1a375fe0d0699dc37d3fe8b8...49f62d75292e384dc9f7a85d72a27c9ffba030d6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">samtools (1.9-6) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Port Python2 script to Python3 using 2to3</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #945735</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Set fields Upstream-Name in debian/copyright.</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Set upstream metadata fields: Repository-Browse.</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Remove obsolete fields Name from debian/upstream/metadata.</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 03 Dec 2019 11:51:08 +0100</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">samtools (1.9-5) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_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="LC14" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/samtools/compare/5b1c474ae5873ebf1a375fe0d0699dc37d3fe8b8...49f62d75292e384dc9f7a85d72a27c9ffba030d6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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="15" 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">@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> pkg-config,</span>
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<td class="diff-line-num new_line" data-linenumber="16" 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="LC16" class="line" lang="plaintext"> tabix (>= 1.0)</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"># tabix is needed for the regression tests.</span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" 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="LC18" 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="LC19" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/samtools</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/samtools.git</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Homepage: http://www.htslib.org/</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">@@ -24,7 +24,7 @@ Package: samtools</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Architecture: any-amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">Recommends: python,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Recommends: python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> cwltool</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Description: processing sequence alignments in SAM, BAM and CRAM formats</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> Samtools is a set of utilities that manipulate nucleotide sequence alignments</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/samtools/compare/5b1c474ae5873ebf1a375fe0d0699dc37d3fe8b8...49f62d75292e384dc9f7a85d72a27c9ffba030d6#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Source: https://github.com/samtools/samtools/archive/1.3.1.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Upstream-Name: SAM tools</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">Files: *</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Copyright: © 2008–2016, Genome Research Ltd. (GRL)</span>
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<a href="https://salsa.debian.org/med-team/samtools/compare/5b1c474ae5873ebf1a375fe0d0699dc37d3fe8b8...49f62d75292e384dc9f7a85d72a27c9ffba030d6#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: Port Python2 script to Python3 using 2to3</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/945735</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: Tue, 03 Dec 2019 11:42:57 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/misc/varfilter.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/misc/varfilter.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC10" 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="LC11" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> # Copyright (C) 2009, 2010 Genome Research Ltd.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -54,7 +54,7 @@</span> import sys</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> import getopt</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> def usage():</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print '''usage: varfilter.py [options] [cns-pileup]</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('''usage: varfilter.py [options] [cns-pileup]</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> Options: -Q INT minimum RMS mapping quality for SNPs</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> -q INT minimum RMS mapping quality for gaps</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -72,7 +72,7 @@</span> Options: -Q INT minimum RMS mapping qual</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> -l INT window size for filtering adjacent gaps</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -p print filtered variants'''</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -p print filtered variants''')</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> def varFilter_aux(first, is_print):</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> try:</span></pre>
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<a href="https://salsa.debian.org/med-team/samtools/compare/5b1c474ae5873ebf1a375fe0d0699dc37d3fe8b8...49f62d75292e384dc9f7a85d72a27c9ffba030d6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">spelling.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">sort-tests-memory-limit.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/samtools/compare/5b1c474ae5873ebf1a375fe0d0699dc37d3fe8b8...49f62d75292e384dc9f7a85d72a27c9ffba030d6#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Changelog: https://raw.github.com/samtools/samtools/HEAD/NEWS</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Name: SAM tools</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> author: ></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Heng Li and Bob Handsaker and Alec Wysoker and Tim Fennell and Jue</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="16" 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">@@ -17,11 +16,12 @@ Reference:</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Repository: https://github.com/samtools/samtools</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> - Name: bio.tools</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> Entry: samtools</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> - Name: SciCrunch</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> Entry: SCR_002105</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> - Name: OMICtools</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> Entry: OMICS_00090</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> Entry: samtools</span></pre>
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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: samtools</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">- Name: SciCrunch</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Entry: SCR_002105</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">- Name: OMICtools</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> Entry: OMICS_00090</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Entry: samtools</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Repository-Browse: https://github.com/samtools/samtools</span></pre>
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