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<div class="content">

<h3 style="margin-top: 20px; margin-bottom: 10px;">

Andreas Tille pushed to branch master at <a href="https://salsa.debian.org/med-team/diamond-aligner">Debian Med / diamond-aligner</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/diamond-aligner/-/commit/634fbddad3bb3c2e427fbce3a74fbba2e40b12e8">634fbdda</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:23:40+02:00 </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: consolidate Github template

</pre>

</li>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/4169b3255a29a3a1c4dafb3ac94c46b478024c88">4169b325</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:24:19+02:00 </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/diamond-aligner/-/commit/428607d0587fb2e0f3021377e4f88494bc3c9531">428607d0</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:24:21+02:00 </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 2.2.5</pre>

</li>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/3c9809a443aadc1c0cb3595cfac336e234642ddc">3c9809a4</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:25:18+02:00 </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/2.2.5'

Update to upstream version '2.2.5'

with Debian dir 43c1fec5d9a5a959bf2ebc5691e01f751789e215</pre>

</li>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/b4a8d1deb93f725a7ed24e3607898300682b02aa">b4a8d1de</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:25:19+02:00 </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: 4.7.4 (routine-update)

</pre>

</li>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/4b448733890bc128a176fa3ef5440e61b781fab4">4b448733</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:25:21+02:00 </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;'>Changes made by cme

</pre>

</li>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/bd6e3fc96506ee5d3b2e18b18c6709f426ab99d3">bd6e3fc9</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:25:22+02:00 </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;'>Drop 'Rules-Requires-Root: no' from d/control (routine-update)

</pre>

</li>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/4962db090bc8af98201ebf572f47564aba17b4bd">4962db09</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T15:25:30+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;'>Set upstream metadata fields: Bug-Database, Repository-Browse.

Changes-By: lintian-brush

</pre>

</li>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/ab8875e4be014160689556a05a1dcdf05cfa7fa9">ab8875e4</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:29:08+02:00 </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;'>Build-Depends: libsqlite3-dev

</pre>

</li>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/f4335b8937b2d8192f09eed7648bd3da9d08d8a7">f4335b89</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:32:20+02:00 </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;'>Upload to unstable

</pre>

</li>

<li>

<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/82c8b501b113a4a5c965d3d05d8f206c996cb443">82c8b501</a></strong>

<div>

<span> by Andreas Tille </span> <i> at 2026-08-13T16:36:51+02:00 </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;'>Drop src/lib/Eigen from d/copyright since upstream stopped shipping this

</pre>

</li>

</ul>

<h4 style="margin-top: 10px; margin-bottom: 10px;">

838 changed files:

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.dockerignore

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.github/workflows/cmake.yml

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.gitignore

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CITATION.cff

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CMakeLists.txt

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Dockerfile

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README.md

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TRADEMARKS

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debian/changelog

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debian/control

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debian/copyright

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debian/upstream/metadata

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debian/watch

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src/ChangeLog

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src/align/align.cpp

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src/align/align.h

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src/align/extend.cpp

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src/align/full_db.cpp

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src/align/gapped_filter.cpp

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src/align/gapped_final.cpp

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src/align/gapped_score.cpp

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src/align/global_ranking/extend.cpp

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src/align/global_ranking/global_ranking.h

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src/align/global_ranking/table.cpp

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src/align/legacy/banded_swipe_pipeline.cpp

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src/align/legacy/pipeline.h

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src/align/legacy/query_mapper.cpp

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src/align/legacy/query_mapper.h

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src/align/load_hits.h

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src/align/output.cpp

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src/align/reseek.cpp

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src/cluster/cluster_registry.cpp

→

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src/align/target.h

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src/align/ungapped.cpp

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src/basic/basic.cpp

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src/basic/config.cpp

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src/basic/config.h

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src/basic/const.h

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src/basic/hssp.cpp

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src/basic/match.h

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src/basic/packed_sequence.h

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src/basic/packed_transcript.h

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