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<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Charles Plessy pushed to branch master at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</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/last-align/-/commit/203ddf7fbb39bf2a355fe987952e3bb4c88d056b">203ddf7f</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T11:50:16+09:00 </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;'>Prepare for new upstream release
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/9291a16b57d8cbb657c94241213655a60afd80fa">9291a16b</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T11:50:44+09:00 </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 1642</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/69046e11a89565b488c1eaf5aa7690a781cee676">69046e11</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T11:50:44+09:00 </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/last-align/-/commit/9c298e36d72b878b55a79919e923d72cb72758c5">9c298e36</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T11:50:46+09:00 </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/1642'
Update to upstream version '1642'
with Debian dir 536e2fad7943bb22d589a759498b78c4b7297655</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/9139a6a06afd96f4f2552d98aff5eb26e8735952">9139a6a0</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T11:50:46+09:00 </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: 4.7.2 (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/3237919ae4d182975cc3e1501977950f700586b6">3237919a</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T11:53:42+09:00 </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;'>routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/2873b488d4f1dc489b9a119856d8c8737634c243">2873b488</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T12:03:31+09:00 </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;'>Refresh patch.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/994c80ab9c63a929045a7ac0e7cbc56ccff2cda0">994c80ab</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T12:03:41+09:00 </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;'>Correct debian/copyright. Thanks, licenserecon
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/ee8a9ed948838d4b6790f7320412caad18cc0c57">ee8a9ed9</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T13:13:11+09:00 </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;'>Better clean the bin/ directory
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/4a4adfbde8e64494d652268e9e8715175e01a762">4a4adfbd</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2025-09-02T13:16:55+09:00 </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;'>Refresh changelog
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
31 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#2eec104bd40706dceb555b7fffb342760f3cbc59">
bin/last-train
</a>
</li>
<li class="file-stats">
<a href="#283f34e3d51a7cafac592c840989299e218a1a99">
bin/maf-linked
</a>
</li>
<li class="file-stats">
<a href="#f3dc1fa2ee7e2641f55cd910fd94c6ac54bac238">
data/MAM4.seed
</a>
</li>
<li class="file-stats">
<a href="#d8808ac5714f9c3554a3d03e80124554c92be191">
data/MAM8.seed
</a>
</li>
<li class="file-stats">
<a href="#056989fd476c60ee978d358e1eb6faa4ca231309">
data/YASS.seed
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#6da0343fd1e96c9faaa35ff4e058c0bb04191144">
doc/last-cookbook.rst
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<li class="file-stats">
<a href="#977fadb853a729d73f897f1532ab693a2edb5af2">
doc/last-seeds.rst
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<li class="file-stats">
<a href="#92d9b0529e219d061bbcde273352ff9d2523754c">
doc/lastdb.rst
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<li class="file-stats">
<a href="#e2f5c323a80f5e4305923d2ba2e2808e90146ccf">
doc/maf-linked.rst
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<li class="file-stats">
<a href="#5e55dbeefff2057b414960d9467d183920e31b8a">
src/Alignment.cc
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<li class="file-stats">
<a href="#bd17e03c676d289c9cc5bb117da6d9d2bde74764">
src/Alignment.hh
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<li class="file-stats">
<a href="#8851e140394897e689075a00e22d69adc336313d">
src/AlignmentPot.hh
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<li class="file-stats">
<a href="#8758dc959aa5524be83960d0bfd56945bc432a26">
src/AlignmentWrite.cc
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<li class="file-stats">
<a href="#175041df6bc020fee30bcd9a8a104c617f1d9feb">
src/LastdbArguments.hh
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<li class="file-stats">
<a href="#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">
src/lastal.cc
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<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">
src/makefile
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<li class="file-stats">
<a href="#c25b47eef38e528e2fca11a7df7ca42c6fe59707">
src/split/cbrc_split_aligner.cc
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<li class="file-stats">
<a href="#6d97945add2df33616de635fdaccd88a502f733c">
src/split/cbrc_split_aligner.hh
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<li class="file-stats">
<a href="#2bf93e35d0ba974fe4be041c601814d14b253461">
src/split/cbrc_unsplit_alignment.cc
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<a href="#fc998af53d94055438c79cc84b23acd0ff926b3f">
src/split/cbrc_unsplit_alignment.hh
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<li class="file-stats">
<a href="#34d9014a0c7348037d434b1f02286a7e8fa59730">
src/split/mcf_last_splitter.cc
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<li class="file-stats">
<a href="#6dffe0a5cd7deaa706cbd6e8ccbeb731f15f4720">
src/split/mcf_last_splitter.hh
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<li class="file-stats">
<a href="#fcd3167fe23623673ee838f0da31855d3d479dff">
test/last-test.sh
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<li class="file-stats">
<a href="#1d0fb87a436fddf5f36b276d9cae7fd11f98e7d9">
<span class="new-file">
+
test/maf-linked-test.sh
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</a>
</li>
<li class="file-stats">
<a href="#62365d6966bf8ca578f9a73e456701094c70407d">
<span class="new-file">
+
test/maf-linked-test.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#1af805d8d4666f01f1acf9d057aa1540064925e0">
<span class="new-file">
+
util/plot-score-matrix
</span>
</a>
</li>
</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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<a href="https://salsa.debian.org/med-team/last-align/-/compare/9a9d806265a0aa921c3a68b3391872de437ef8a2...4a4adfbde8e64494d652268e9e8715175e01a762">View it on GitLab</a>.
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Notification message regarding https://salsa.debian.org/med-team/last-align/-/compare/9a9d806265a0aa921c3a68b3391872de437ef8a2...4a4adfbde8e64494d652268e9e8715175e01a762 at 1756786881
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