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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/b69c70cd5d63a0a22b89c6888e7dc524495b2f92">b69c70cd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-03T12:13:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.13.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/d62f69e376f39fda1171b9082aedec0b4fd01202">d62f69e3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-03T12:13:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.2.13.2'
Update to upstream version '1.2.13.2'
with Debian dir 6b1ec91029816a90c53862c3a1e13cda5b68d8d3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/cdb551f5d2af7f11221c6a0f8728ae34276ade0d">cdb551f5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-03T12:13:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/1d7d7f2b03e4fb32cb0e1ec2b56c8d9654608508">1d7d7f2b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-03T12:15:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/ca90f19cb6d8533f87fd360b8f77d276514d4fff">ca90f19c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-03T12:15:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/fa31afcf165faf4970941e0487f37c905d636b39">fa31afcf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-03T13:17:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">For some reason the -Xmx argument will be dropped when constructing the java call. Just drop it from the test as well.
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
</a>
</li>
<li class="file-stats">
<a href="#8875df48c18030126ef5ef5a6f5c93b23451fb9f">
MANIFEST.in
</a>
</li>
<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
</a>
</li>
<li class="file-stats">
<a href="#5f496f892af6f1236d52a40e93f45d806a0f0dfb">
bin/bam_pipeline
</a>
</li>
<li class="file-stats">
<a href="#c97c24edf662577079bed651de857bc30f1cf0e0">
bin/bam_rmdup_collapsed
</a>
</li>
<li class="file-stats">
<a href="#905961633af05fef6692b1ebeb4ec32b98525430">
bin/conv_gtf_to_bed
</a>
</li>
<li class="file-stats">
<a href="#0efc9369c10b53533cebc499e82cdfca13b2eee7">
bin/paleomix
</a>
</li>
<li class="file-stats">
<a href="#eabc3765a6620b86864030ad697bc646bc47822f">
bin/phylo_pipeline
</a>
</li>
<li class="file-stats">
<a href="#70129b06e60cc1aa923380f66527099c89c2507d">
bin/trim_pipeline
</a>
</li>
<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="#f328292d7bb6c225edf642ef4e25b4ff7a6845ce">
<span class="new-file">
+
debian/patches/adapt_java_calling_test.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#6dda527a39d66bc2c4dd86a7972b86212e1dff87">
debian/patches/avoid_downloading_prerequisites.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#a259c04ac2ca00c04be3cdef20e96553c1ba99d2">
docs/bam_pipeline/filestructure.rst
</a>
</li>
<li class="file-stats">
<a href="#254a2da7a740675e537439eb88e32083b9ea4771">
docs/conf.py
</a>
</li>
<li class="file-stats">
<a href="#d0153cac95479af9bfb99b746b633bc8255bb53a">
docs/index.rst
</a>
</li>
<li class="file-stats">
<a href="#ee0d43c053e0872e8b523e48e91f728049747f57">
misc/setup_bam_pipeline_example.sh
</a>
</li>
<li class="file-stats">
<a href="#cbbac29c80466534d34fc670e78b00d0c6b015b0">
misc/setup_phylo_pipeline_example.sh
</a>
</li>
<li class="file-stats">
<a href="#5bb191d04629cdee31c9772e55168d47d9ce56d7">
misc/skeleton.py
</a>
</li>
<li class="file-stats">
<a href="#ad7c5e26ed27c61530bdd1096c6b004bced813fa">
misc/synthesize_reads.py
</a>
</li>
<li class="file-stats">
<a href="#31db6545668043f26d9d05b8338b53acf3b3c5e1">
paleomix/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#df89aec0712464da4da1613415f0ec1b019ec6a3">
paleomix/atomiccmd/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#37a3113a19f87e3f2e4a83827cd4f68a9d1bf5cd">
paleomix/atomiccmd/builder.py
</a>
</li>
<li class="file-stats">
<a href="#346d3dc8ea9623e13fafc5998c1230f9e55e736f">
paleomix/atomiccmd/command.py
</a>
</li>
<li class="file-stats">
<a href="#d8017f4b9be68f963ff9b8fc63c80795c351fc2f">
paleomix/atomiccmd/pprint.py
</a>
</li>
<li class="file-stats">
<a href="#9caf62a5b3ead0d3e988552c62f85604573a1b20">
paleomix/atomiccmd/sets.py
</a>
</li>
<li class="file-stats">
<a href="#011e0b90b44378da7641a4758ff0693fa8d0c9a3">
paleomix/common/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#a2d5f8d43fd013fb02fe1d9fd90f2be5335ae684">
paleomix/common/bamfiles.py
</a>
</li>
<li class="file-stats">
<a href="#e55805e7d33eaef5c399d5e88065e6240ea7e248">
paleomix/common/bedtools.py
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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