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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/hisat2">Debian Med / hisat2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/b522577df45e0a568a5ed48a8385d019f363d7a7">b522577d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T19:03:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use the libsimde-dev package instead of our code copy.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/6a7760ab29a956706353b5c4adeb6b6f83825963">6a7760ab</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T19:03:13+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/hisat2/-/commit/c5f5afab95bc8b7f9e25600e364be7146ebf1e9a">c5f5afab</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T19:03:13+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/hisat2/-/commit/3bbba4b9bf1cc3d537eb5427ff5fd0c5d2da1bf8">3bbba4b9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T19:03:13+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/hisat2/-/commit/aa522f5567bcdf3795d2930b018556211b90b246">aa522f55</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T19:03:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream moved to GitHub
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/21cc27e3bb783290639912729602853c69de75e2">21cc27e3</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T19:03:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use the HISAT2 citation instead of the HISAT paper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/77c7ef83b19c1f3aa3498b8a8e2b5de30d49d323">77c7ef83</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T19:54:48+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/hisat2/-/commit/0757bbf4224be0781fe5099fdb28d436f90e18b2">0757bbf4</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T19:54:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/0dd8e06d554150afb141ea10de5a49838bdfc1b4">0dd8e06d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T19:55:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.2.0'
Update to upstream version '2.2.0'
with Debian dir d0fddf93d01d715265b52e3ddceac332d0e32257</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/7468f313037948e455b5f7db4e127fcaf872afd6">7468f313</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T20:07:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Freshen the patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/3c722592e3e574284309eae0fdb5a134f88b765f">3c722592</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T20:11:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/1b4fac2f2ff0b808c2633788d78959b438d29fa1">1b4fac2f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T20:26:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added patch to fix the manual path
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/a63d242098083b0f09fb681b7e7d875e7ad18741">a63d2420</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-19T23:04:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">2.2.0-1
</pre>
</li>
</ul>
<h4>24 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#24139dae656713ba861751fb2c2ac38839349a7a">
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.gitattributes
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
<span class="new-file">
+
.gitignore
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
<span class="new-file">
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CMakeLists.txt
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<li class="file-stats">
<a href="#58b87e402d3f929514834a4b9a514eb25e828036">
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HISAT2-genotype.png
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<li class="file-stats">
<a href="#f11fb3bba37e7060bedcd5895812b7c511c52651">
MANUAL
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<span class="new-file">
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README.md
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<li class="file-stats">
<a href="#d814d3e7d55ad64b9a68fdab60bd5741a6c86453">
TUTORIAL
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<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#cd089ae45ce870c45e434019e8f1ed4f066cd425">
<span class="new-file">
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_config.yml
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<li class="file-stats">
<a href="#484d91097026f1eb4f1a83445d9e9474d08cb0b8">
aligner_result.cpp
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<li class="file-stats">
<a href="#e61d74ca26201e13b6daf686712a607420c3dcbe">
aligner_result.h
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<li class="file-stats">
<a href="#4a2f17018c715a92c326e378d8da0ae393f66566">
aligner_seed2.h
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<li class="file-stats">
<a href="#5301e199e78169c5669ce001f437d3fa76accc21">
aligner_sw.cpp
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<li class="file-stats">
<a href="#057e0784d807c7b84958635ddeeb5003f2751ece">
aln_sink.cpp
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</li>
<li class="file-stats">
<a href="#5caf7b101f4ba008ee8d93f74a20baefcf2b451a">
aln_sink.h
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<li class="file-stats">
<a href="#23fe7d40df390744370c0e80c2bcc72a078c6b0a">
alphabet.cpp
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<li class="file-stats">
<a href="#4204129a7062084f1ce66ea879026cee5da13862">
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bit_packed_array.cpp
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<li class="file-stats">
<a href="#86ac26cb7b4343eeb657356281779e1a3e9d7d30">
<span class="new-file">
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bit_packed_array.h
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<li class="file-stats">
<a href="#03d5fe68cb76a542cb9c06b8e03093e21319ca35">
blockwise_sa.h
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<li class="file-stats">
<a href="#43da7ca426ad4565891f6a801f296b836b95fce5">
<span class="deleted-file">
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classifier_li.h
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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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<li class="file-stats">
<a href="#e33a359b2250338a44f94e503c89a57a2fcf0a61">
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−
debian/include/simde/check.h
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</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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