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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/salmon">Debian Med / salmon</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/5b2d6af5aa4c81f2da505a3225977b5444b41927">5b2d6af5</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-06-05T08:45:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add a patch for portable pausing in spinlocks.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/fffdef8ec5b4911c594e60303ceea5cf2ce25e29">fffdef8e</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-06-05T08:45:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/upstream/metadata: link to upstream's repository
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/115b394f77fdddac637755b1983efb0da3e2cddb">115b394f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-16T12:43:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.0+ds1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/3450efa7fe1de7f3c2a55f3ea0a7fbfc7cf3b275">3450efa7</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-16T12:43:13+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/salmon/-/commit/19edcb995d6c059dce8676393a12442d1f74102a">19edcb99</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-16T12:43:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.3.0+ds1'
Update to upstream version '1.3.0+ds1'
with Debian dir 4d091545e07fbf2b6c031f3e85c13b7b7e0e7671</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/806f5cfbb5db102f709a51e6c74dffe9f15863d9">806f5cfb</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-16T12:43:17+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/salmon/-/commit/b4670f5f0fdaf4c61f5b98be6f7280129ca2e698">b4670f5f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-16T12:47:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">kseq patch no longer needed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/b3ba025bac81ed5b94b8f48c32c791c43d5c9d42">b3ba025b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-07-16T13:06:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">needs libgff-dev > 2
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#34ffb03041dc818ba71da0518ec52a0134f543f8">
current_version.txt
</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="#9d49b6d883b0ee8a9df68d140bf8cf1c364bf076">
debian/external/pufferfish/include/FastxParserThreadUtils.hpp
</a>
</li>
<li class="file-stats">
<a href="#bae08dca7af50ae6494331a147cd30150ecb5714">
debian/patches/disable-version-check.patch
</a>
</li>
<li class="file-stats">
<a href="#d9355830e2eda69faabbef1088bf6f9d94b7e771">
<span class="deleted-file">
−
debian/patches/kseq
</span>
</a>
</li>
<li class="file-stats">
<a href="#0a8d7c289bbb6d9bb3feec5aa0f3e4068bbee285">
<span class="new-file">
+
debian/patches/portable_pause
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
debian/patches/spelling
</a>
</li>
<li class="file-stats">
<a href="#ee54dc79014b3def963898e50c98877d46c6b27e">
debian/patches/use_debian_packaged_libs.patch
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#9d4e8ab62832d7b298261aae1fe1123d28783525">
doc/source/conf.py
</a>
</li>
<li class="file-stats">
<a href="#8ffde13df31f212345642ccfa4755f3bd99e7e61">
docker/Dockerfile
</a>
</li>
<li class="file-stats">
<a href="#3cbc10c17d78796adbdc9a8a8b8702f83a02d41f">
docker/build_test.sh
</a>
</li>
<li class="file-stats">
<a href="#2bc7c7c64784b968b1404d3f09805fe683f980b1">
include/AlevinOpts.hpp
</a>
</li>
<li class="file-stats">
<a href="#5cef8fa5ec1ece7a48a7915ced5deaf811bf19f5">
include/AlignmentLibrary.hpp
</a>
</li>
<li class="file-stats">
<a href="#2ac0e90145df8287bf8f2694a3e2af65d0939b0b">
include/AtomicMatrix.hpp
</a>
</li>
<li class="file-stats">
<a href="#80185316fe3b1f661a84dc01d133b5fb610d6061">
include/BAMQueue.hpp
</a>
</li>
<li class="file-stats">
<a href="#190d99cc5ab950958653ebc379ba8a35f8e86031">
include/BAMQueue.tpp
</a>
</li>
<li class="file-stats">
<a href="#ba21e28a4a0fb90d1a8bc698ffc1d6360721d2ef">
include/CollapsedCellOptimizer.hpp
</a>
</li>
<li class="file-stats">
<a href="#b520c211a6c8edb6997dae1a17e2684187d91e8a">
include/CollapsedEMOptimizer.hpp
</a>
</li>
<li class="file-stats">
<a href="#c30173959eead2de523cc996d8c2bb852a427b62">
include/CollapsedGibbsSampler.hpp
</a>
</li>
<li class="file-stats">
<a href="#54e7c89c31efd77245f0e28769a95f9f9065879e">
include/DistributionUtils.hpp
</a>
</li>
<li class="file-stats">
<a href="#a3e07d2ed2be80b241300903096d45955b061bb5">
include/EMUtils.hpp
</a>
</li>
<li class="file-stats">
<a href="#2f4c95e51d181930dcddc9dbaeac2063cd1c62d8">
include/FragmentLengthDistribution.hpp
</a>
</li>
<li class="file-stats">
<a href="#96a6d349faec8965a43df7703931ac525f2a6234">
include/FragmentStartPositionDistribution.hpp
</a>
</li>
<li class="file-stats">
<a href="#f05db237f9b821f31941b5ede8a2c432d8736b61">
include/GZipWriter.hpp
</a>
</li>
<li class="file-stats">
<a href="#1cb3b42bfac5c65f32a988f2794fbda76a880ef5">
include/SBModel.hpp
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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