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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Michael R. Crusoe pushed to branch master at <a href="https://salsa.debian.org/med-team/bwa-mem2">Debian Med / bwa-mem2</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/c2d57ddff982e1618ea014fd66db6fc7833c0cac">c2d57ddf</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:15:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/watch: upgrade to uscan 5 syntax
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/301d7c25756cff88edb251de5cea1ac8a98ac3f5">301d7c25</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:16:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/55c9645371d54c6432da0e2758b0d22d74baf9c1">55c96453</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:16:36+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.3</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/9b5419491947d0c433dca02d32b8b589b08e71ee">9b541949</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:16:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/2.3'
Update to upstream version '2.3'
with Debian dir 373c4c2b2c508f661f4703751afc9bc802394981</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/2f2f5eca22f71ffa2de0b0d0f89a6ad27e54237a">2f2f5eca</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:16:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.7.3 (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/1c373b4d4a3e465cb80f91277baac9f5f8f0a7d0">1c373b4d</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:16:49+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>debputy lint --auto-fix (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/5fd0f5a20af36c29abb37ec18bdc13aa7f0fd7e4">5fd0f5a2</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:37:03+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Removed many patches that were applied upstream.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/851a1b27d35cffb17a4f18746aa89b92000084e8">851a1b27</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:56:01+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Add +ds suffix, as we removed the ".git" directory from the upstream tarball.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/1496a7383bba808fc6cb110d4f391b8cb5cdc9c5">1496a738</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:56:09+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.3+ds</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/9c11e917adc8260e63cc67fd876678ab2a626bb4">9c11e917</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T10:56:10+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/2.3+ds'
Update to upstream version '2.3+ds'
with Debian dir 6f61ef157a3bbb5a06d668e344a2c5688f259652</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/22adbd0563e2bfb07dfc3c45053eade35a64471e">22adbd05</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T11:44:34+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>d/clean: enable repeat builds
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bwa-mem2/-/commit/dd8a0c95ed0f9e379077d3ae7ac44dad6e80e1b1">dd8a0c95</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-02-21T11:44:34+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>copyright updates
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
23 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">
<span class="new-file">
+
debian/clean
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#7b3faa13a908c9409e43232f4407645c7e50d8c3">
<span class="deleted-file">
−
debian/patches/0001-Fix-typo.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#5f182aa55b40ea6944e52da9719fd8b5fe6c6e0e">
<span class="deleted-file">
−
debian/patches/0002-fixed-return-status-due-incorrect-input-files.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#3bf17829d17b9486fdb43c0e14f5696731ecad7b">
<span class="deleted-file">
−
debian/patches/0003-fixed-smem-memory-rellocation-issue-issue167.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#f4cec0723132f714d53f11ee0b489b96c55fd93e">
<span class="deleted-file">
−
debian/patches/0004-Update-to-reflect-2.2.1-release-and-small-typo.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bfdb6d23322e1d26f4e955844192d3d6d3c65707">
<span class="deleted-file">
−
debian/patches/0005-GCC-11-now-defines-__rdtsc-so-definition-test-condit.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#d6505054ff9b9105f96001e0e6ce650e801b9016">
<span class="deleted-file">
−
debian/patches/0006-fixed-segfault-due-to-memory-shortage-in-smem.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#0b6e657471469120f27e7b0aecf78d1347e136ca">
<span class="deleted-file">
−
debian/patches/0007-Merge-pull-request-229-from-gh-jphan-fix_n_processed.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
debian/patches/hardening
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#41600a842dba57308a0d79bc96693da2a165d3f1">
src/bwamem.cpp
</a>
</li>
<li class="file-stats">
<a href="#a8fec4dd53ea6accda8899eebd877f2826250abe">
src/bwamem.h
</a>
</li>
<li class="file-stats">
<a href="#f1ed99eb0756fd32fb90931d91ada7feddb4aa8f">
src/fastmap.cpp
</a>
</li>
<li class="file-stats">
<a href="#637402f267101e3215493309f6f6eca660080376">
src/kthread.cpp
</a>
</li>
<li class="file-stats">
<a href="#7646997a0df029ff45982a5c717d133060e0d87b">
src/macro.h
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<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
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<a href="#995ba3c8bc840c8be24c00c58219dc888b55d44b">
src/utils.h
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</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>
</div>
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—
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<a href="https://salsa.debian.org/med-team/bwa-mem2/-/compare/7151fe2fea4918da6ae48327ba3895f65b684857...dd8a0c95ed0f9e379077d3ae7ac44dad6e80e1b1">View it on GitLab</a>.
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