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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Steffen Möller pushed to branch master at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/9d8309b8dd271d1f2d55965adb7d6fe6b9c42b28">9d8309b8</a></strong>
<div>
<span> by Steffen Moeller </span> <i> at 2026-02-22T15:11:39+00:00 </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/bowtie2/-/commit/ea62608187cc1b15ab7a2fc42d537fcaa06f0efe">ea626081</a></strong>
<div>
<span> by Steffen Moeller </span> <i> at 2026-02-22T15:11:40+00:00 </i>
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<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 2.5.5</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/737e3df9e66748cfba04efe99f60a35d23db3408">737e3df9</a></strong>
<div>
<span> by Steffen Moeller </span> <i> at 2026-02-22T15:12:04+00:00 </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/2.5.5'
Update to upstream version '2.5.5'
with Debian dir 8afaf582c63f7aaf78be2b11472e8aae96f6ef88</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/4dfdc152fffd22aebcedacc910e3539ccc233681">4dfdc152</a></strong>
<div>
<span> by Steffen Moeller </span> <i> at 2026-02-22T15:12:04+00:00 </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/bowtie2/-/commit/1f513ffee91623e4c8d221465f692d9e99753a0c">1f513ffe</a></strong>
<div>
<span> by Steffen Moeller </span> <i> at 2026-02-22T15:47:04+00:00 </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 2.5.5.
</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
37 changed files:
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<li class="file-stats">
<a href="#32e7b86fef2d14e50d14716af4894aac7779f716">
.github/workflows/random-tests.yml
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<li class="file-stats">
<a href="#7a37717622fd6c0538b1b8776cdd4e30d3a990c8">
.github/workflows/simple-tests.yml
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</li>
<li class="file-stats">
<a href="#dea7d9d2c0ed0c505374f9f90877bedd8f077710">
BOWTIE2_VERSION
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</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#f11fb3bba37e7060bedcd5895812b7c511c52651">
MANUAL
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<li class="file-stats">
<a href="#465370da702349b6dcb3f9f2026872cad6877efa">
MANUAL.markdown
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</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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</li>
<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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</li>
<li class="file-stats">
<a href="#a177c5447e9cdcbfd7d1dc1c7140293d0cfbc779">
aligner_seed.cpp
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</li>
<li class="file-stats">
<a href="#c9b466ab26199558112972a17a75b8c21ac85c19">
aligner_seed.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="#9b9c3e8e49dbc147620bdc9c0e3d970e5ee41ea9">
aligner_sw_driver.cpp
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<li class="file-stats">
<a href="#00039f110c5d0733f8b233ea89fa70f5ffe054aa">
aligner_sw_driver.h
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<li class="file-stats">
<a href="#5caf7b101f4ba008ee8d93f74a20baefcf2b451a">
aln_sink.h
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</li>
<li class="file-stats">
<a href="#464ce98392db4e108605b7a12696e7c3434eaf56">
bowtie2-build
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</li>
<li class="file-stats">
<a href="#622d3bcfba0df0e4ae8a0849416ed2d2cf987528">
bowtie2-inspect
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</li>
<li class="file-stats">
<a href="#2a41b09048713a7b4d365bbacd93f3d6ec5b764e">
bowtie_main.cpp
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</li>
<li class="file-stats">
<a href="#6026283a643bf7fb08c2ef0b797486df93cf0698">
bt2_search.cpp
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</li>
<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="#8349e79c83e3dffc4d4ae366712ef4e351aebe80">
debian/patches/correct_64bit_test
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</li>
<li class="file-stats">
<a href="#3ab00da70db0f997a696f5703a50cd50fe504347">
debian/patches/do-not-rebuild-during-test.patch
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<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
debian/patches/hardening.patch
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<li class="file-stats">
<a href="#41edb87d75827ea69fc4be16c1d2830db9a0eb81">
debian/patches/no_sanity
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<li class="file-stats">
<a href="#76258ff6f1526200cf3fda90e9f37fd9ee4b4364">
debian/patches/reproducible.patch
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<a href="#6815d1260ed0fdc6f0d97bc028700b124f2bf358">
debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
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</li>
<li class="file-stats">
<a href="#64628a335264e9862b9b687ae70cddf5e153ea9b">
debian/patches/use-source-date-epoch-in-Makefile.patch
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<li class="file-stats">
<a href="#ccc364c6c660e798a4f3c3b78119cbea257aee1e">
doc/manual.html
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<li class="file-stats">
<a href="#a1ba375e8deab5b12b1347797835e927dca95425">
doc/website/manual.ssi
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<li class="file-stats">
<a href="#9485aa1b2c39982f48264019fde0712132ed80f5">
doc/website/recent_news.ssi
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<li class="file-stats">
<a href="#59bf596910fb7006481a4d8a45de81ff2bd75a4d">
doc/website/rhsidebar.ssi
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</li>
<li class="file-stats">
<a href="#628e684829af2d14bddc3e5d3fc6f30fea5fb1ca">
group_walk.h
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</li>
<li class="file-stats">
<a href="#50b0e95b63ccb2c46e008fda8904d780b714df41">
opts.h
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<a href="#7c4ae52e4a13c990d16c9530fb874ed79064a5cd">
pat.cpp
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</li>
<li class="file-stats">
<a href="#6c8922e214bc665a49b5acea11b505cbd36446c5">
pat.h
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<li class="file-stats">
<a href="#feeebf6c8e249c25303af46ea1abd54e5f54b5db">
processor_support.h
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The diff was not included because it is too large.
</h5>
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