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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/paleomix">Debian Med / paleomix</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/f1321f2f267d6cb9ee01bc8889e7e44e29fa8c4f">f1321f2f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T07:57:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/8daace9faa9d4bdbcb748e90a58d73e33fb5b742">8daace9f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T07:57:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/8d194931bc4e948bb00c3a65160384720a09363a">8d194931</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T07:57:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.3.0'
Update to upstream version '1.3.0'
with Debian dir d52df7347cea01ad46f4ea1f04e28598d0b41af8</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/a517f1124461c3f75527980e4e56d49097f53568">a517f112</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T07:57:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/3548bdcb7ba13c8192c15d3de765c15c3a6edcfc">3548bdcb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T07:57:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/89649b7c955ce22ef214b8c64467eb36f9506ecb">89649b7c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T08:08:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/f84833f68aebebe3414ab8777fe24f03e2cfb7c8">f84833f6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T08:15:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New version supports Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/ae5f75acebd9f0c9ec7d5203fc6c6339b5f65fbc">ae5f75ac</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T08:15:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/0aa23a2aa1b7d93585289920d3089b42c86cfa16">0aa23a2a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T08:15:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/ee2d42932e8cbee37194c5b002bddf0f298d40c4">ee2d4293</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T08:24:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream switched from nose to pytest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/38bac3cd585d3d7deebff8d1c9619df01bbc4bca">38bac3cd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T08:35:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust (Build-)Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/d94c2c86c755810d814202167aa21a240aeff166">d94c2c86</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-01T08:54:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some tests
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
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<li class="file-stats">
<a href="#eff4cd4a1e08155d42c85e48787c9e4c288b8d02">
tests/.coveragerc
→
.coveragerc
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<a href="#3374c1c18de688d968548dc001e40ee700f04f6f">
<span class="deleted-file">
−
INSTALL.rst
</span>
</a>
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<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
licenses/mit.txt
→
LICENSE
</a>
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<li class="file-stats">
<a href="#8875df48c18030126ef5ef5a6f5c93b23451fb9f">
MANIFEST.in
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<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<li class="file-stats">
<a href="#5f496f892af6f1236d52a40e93f45d806a0f0dfb">
<span class="deleted-file">
−
bin/bam_pipeline
</span>
</a>
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<li class="file-stats">
<a href="#c97c24edf662577079bed651de857bc30f1cf0e0">
<span class="deleted-file">
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bin/bam_rmdup_collapsed
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<li class="file-stats">
<a href="#905961633af05fef6692b1ebeb4ec32b98525430">
<span class="deleted-file">
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bin/conv_gtf_to_bed
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</li>
<li class="file-stats">
<a href="#0efc9369c10b53533cebc499e82cdfca13b2eee7">
<span class="deleted-file">
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bin/paleomix
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<li class="file-stats">
<a href="#eabc3765a6620b86864030ad697bc646bc47822f">
<span class="deleted-file">
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bin/phylo_pipeline
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<a href="#70129b06e60cc1aa923380f66527099c89c2507d">
<span class="deleted-file">
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bin/trim_pipeline
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<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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<a href="#f328292d7bb6c225edf642ef4e25b4ff7a6845ce">
<span class="deleted-file">
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debian/patches/adapt_java_calling_test.patch
</span>
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<a href="#6dda527a39d66bc2c4dd86a7972b86212e1dff87">
<span class="deleted-file">
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debian/patches/avoid_downloading_prerequisites.patch
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<a href="#03cce9526b9236ae11584cbaa2b92539d969a6a6">
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debian/patches/avoid_privacy_breach.patch
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<a href="#2e588138bba8c644faa3b7daf57c531266333767">
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debian/patches/exclude_failing_test.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
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debian/salsa-ci.yml
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<li class="file-stats">
<a href="#0fdbda66ca3b7b0b45b2a4108379ad19f7923a9e">
docs/bam_pipeline/configuration.rst
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<a href="#a259c04ac2ca00c04be3cdef20e96553c1ba99d2">
docs/bam_pipeline/filestructure.rst
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<a href="#9b975bd2ff9693c7c71cb9a30c6315d7e1196d43">
docs/bam_pipeline/index.rst
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<a href="#bdbed2cbd88d3bb7d47c29d5bb99a3214a39ec6c">
docs/bam_pipeline/makefile.rst
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<a href="#7cb682e76bde2cb9190cebd3988bd33952e473b2">
docs/bam_pipeline/makefile.yaml
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<a href="#e5368178d38862b612c03eac3e417a38b54bc3b6">
docs/bam_pipeline/overview.rst
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<a href="#37106ac55933b60ea232abb2c9bb974138d9da0b">
docs/bam_pipeline/requirements.rst
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<a href="#19d875d2f02769cf6d8972936b903f6bd24332ea">
docs/bam_pipeline/usage.rst
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<h5>The diff was not included because it is too large.</h5>
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