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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/671a62e0a0a74fcae9e3ad6befc5e3074687c470">671a62e0</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T18:38:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">prep for update
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/b49c11bea46a229f2575d11da6be8151ce946ff5">b49c11be</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T18:38:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/ab957f553b533fbeefb980da89ff85507b9742b5">ab957f55</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T18:38:19+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/bowtie2/-/commit/b1b4187f92146be1134a763287d90ac6aa648325">b1b4187f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T18:38:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/b6f6e46bfd6bfa87b0ff51402d09d6e1b37f1b2f">b6f6e46b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T18:38:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.4.4'
Update to upstream version '2.4.4'
with Debian dir 1f0c94300dbd49df3da4e08187c0ed18a34a6693</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/e042b6d57194598c43f28c58457d300e1fe3ad5c">e042b6d5</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T18:38:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/137ce265b6bb57fc7caf1c8ca49a097a5506c02e">137ce265</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T18:46:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/1564432fac799573e9278b81939f5ae3a8cda27e">1564432f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T19:00:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">no more tinythread, it seems
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/a26af0e2d88ccfb7e65b80d82684c33c8c7d8db7">a26af0e2</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T19:00:37+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>18 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7e43d6808132163da1c92d84bb5c6a900737fe4b">
<span class="new-file">
+
.github/workflows/bowtie2.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
.gitmodules
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#dea7d9d2c0ed0c505374f9f90877bedd8f077710">
BOWTIE2_VERSION
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#f11fb3bba37e7060bedcd5895812b7c511c52651">
MANUAL
</a>
</li>
<li class="file-stats">
<a href="#465370da702349b6dcb3f9f2026872cad6877efa">
MANUAL.markdown
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#b0498d416b96de2df468eef24daddcb39e8ff0da">
aligner_cache.cpp
</a>
</li>
<li class="file-stats">
<a href="#d0b93e802a57a9f254ad87c9890869508854e2e3">
aligner_cache.h
</a>
</li>
<li class="file-stats">
<a href="#c9b466ab26199558112972a17a75b8c21ac85c19">
aligner_seed.h
</a>
</li>
<li class="file-stats">
<a href="#dcd94af6e4b1cb5e67bce841e17f29eb32c71e89">
aligner_sw_common.h
</a>
</li>
<li class="file-stats">
<a href="#db01803ecfdff4ed1bbcf3e3443f63b68e3f1772">
aligner_swsse_ee_u8.cpp
</a>
</li>
<li class="file-stats">
<a href="#3e7769daf37e90f12e6fec195d569fd348ebd24e">
aligner_swsse_loc_u8.cpp
</a>
</li>
<li class="file-stats">
<a href="#5caf7b101f4ba008ee8d93f74a20baefcf2b451a">
aln_sink.h
</a>
</li>
<li class="file-stats">
<a href="#03d5fe68cb76a542cb9c06b8e03093e21319ca35">
blockwise_sa.h
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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