<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en" style='--code-editor-font: var(--default-mono-font, "GitLab Mono"), JetBrains Mono, Menlo, DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<title>
GitLab
</title>

<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>


<style>img {
max-width: 100%; height: auto;
}
body {
font-size: .875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px;
}
body {
font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px; font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";'>
<div class="content">

<h3 style="margin-top: 20px; margin-bottom: 10px;">
Michael R. Crusoe pushed to branch upstream at <a href="https://salsa.debian.org/med-team/libwfa2">Debian Med / libwfa2</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/libwfa2/-/commit/89967301d3c6930b9ed04a313e31929d13cc1ddb">89967301</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2026-04-30T09:14:19+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 2.3.6</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
103 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#d378bb48fcfbb9f46e6efa808bf296646db58bf1">
<span class="new-file">
+
.github/workflows/make.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
<span class="deleted-file">

VERSION
</span>
</a>
</li>
<li class="file-stats">
<a href="#9266624b881ae43f2b64a389484ea9e0754afaa6">
<span class="new-file">
+
VERSION.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#52eefe5268cf1947262006e14c42dfc987f00b1e">
alignment/Makefile
</a>
</li>
<li class="file-stats">
<a href="#22c0f45163353edb981898f7945dd9c9ac3e0dd4">
alignment/cigar.c
</a>
</li>
<li class="file-stats">
<a href="#03523d05e34b3c457e6c6f03d408c9675cb20948">
alignment/cigar.h
</a>
</li>
<li class="file-stats">
<a href="#b66844e8693593dae797c624c6fa0e60cd603b13">
<span class="new-file">
+
alignment/cigar_utils.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#f1969ccd09d239ac813885f644eb493b8bd5c02f">
utils/string_padded.h

alignment/cigar_utils.h
</a>
</li>
<li class="file-stats">
<a href="#d18cf7892c6c443da48526cfc6bb74e7a90f9f5b">
alignment/score_matrix.c
</a>
</li>
<li class="file-stats">
<a href="#6ea80f29849368e8b08690d08b51f6722f2606c6">
bindings/cpp/WFAligner.cpp
</a>
</li>
<li class="file-stats">
<a href="#6b54b3c22a02ab5926c4cb3c0ec8694c437376a8">
bindings/cpp/WFAligner.hpp
</a>
</li>
<li class="file-stats">
<a href="#396f390c5d3f55143680ee1298e83a8bd968ce6f">
examples/Makefile
</a>
</li>
<li class="file-stats">
<a href="#f60a85545843792e91807e2d180f2978014e8c79">
examples/wfa_basic.c
</a>
</li>
<li class="file-stats">
<a href="#a18869b8dd6fd73f3b1454613e25e63dc9433310">
examples/wfa_bindings.cpp
</a>
</li>
<li class="file-stats">
<a href="#e415324b5aa03dab5165b402aee78c10bb224eba">
examples/wfa_lambda.cpp
</a>
</li>
<li class="file-stats">
<a href="#8830c9ed5fb31e949b61cb9b0e6e4a49f2d44d55">
guix.scm
</a>
</li>
<li class="file-stats">
<a href="#ae1813a8d498a10c7802e335da89fa1c60bf7403">
<span class="new-file">
+
img/wfa.endsfree.png
</span>
</a>
</li>
<li class="file-stats">
<a href="#f1e2dc3769a13d0e3a4a9087ad49ff57f91b668c">
<span class="new-file">
+
libwfa2.pc.in
</span>
</a>
</li>
<li class="file-stats">
<a href="#096b0f7fad97c7ee0ea375206c8a137543510935">
scripts/wfa.alg.cmp.score.sh
</a>
</li>
<li class="file-stats">
<a href="#e2e3b03064aedec049bc2f3300d6c8901e1699f9">
system/mm_allocator.c
</a>
</li>
<li class="file-stats">
<a href="#ae9dee31edbb20ee662dbc60e30e39daf9f35214">
system/mm_allocator.h
</a>
</li>
<li class="file-stats">
<a href="#797d7f588a283fb14df34af2d94061622e7c7a59">
system/mm_stack.c
</a>
</li>
<li class="file-stats">
<a href="#35b3ef6024fa31bbb9218dc892047749d9d67314">
system/profiler_counter.h
</a>
</li>
<li class="file-stats">
<a href="#3ad013793c68126b4d075edecefc6cc40572d5e3">
system/profiler_timer.h
</a>
</li>
<li class="file-stats">
<a href="#3f611bd8583e484a7015ea7282f3643d93ff2665">
tests/wfa.utest.check/wfa.utest.log
</a>
</li>
<li class="file-stats">
<a href="#6d8caa7fb3a95b190534c8577e5cbca0b6fad7d1">
tests/wfa.utest.check/wfa.utest.log.mem
</a>
</li>
<li class="file-stats">
<a href="#7431549ee9d2799388ffac4a884046538fa09c91">
tests/wfa.utest.check/wfa.utest.log.time
</a>
</li>
<li class="file-stats">
<a href="#549b29b19a794db749b9069def97f128be86e550">
<span class="new-file">
+
tests/wfa.utest.clean.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#eef4b80bad7aab49b4d451414e50a0c5f1014889">
tests/wfa.utest.cmp.sh
</a>
</li>
<li class="file-stats">
<a href="#69e9d06086164c0fdcda2ee20c544d00cff8170c">
<span class="deleted-file">

tests/wfa.utest.performance.cmp.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#c0a812ebb9858d86e3633eb1664b2c8205343b74">
tests/wfa.utest.performance.sh
</a>
</li>
<li class="file-stats">
<a href="#555bd375d673819c1e438febd754de631bec9b12">
tests/wfa.utest.sh
</a>
</li>
<li class="file-stats">
<a href="#4a1150a9ca413cb7a4727c8aae4b190975047d4a">
tests/wfa.utest.valgrind.sh
</a>
</li>
<li class="file-stats">
<a href="#016dda517e72724ec564390944eba9d67055cefc">
tools/README.md
</a>
</li>
<li class="file-stats">
<a href="#cf6c7257ec5e5013ac9631ed9decc6338a249e1d">
tools/align_benchmark/Makefile
</a>
</li>
<li class="file-stats">
<a href="#e2ab8d05db383380a0f562f328b1db6b22af2797">
tools/align_benchmark/align_benchmark.c
</a>
</li>
<li class="file-stats">
<a href="#f84d14a4703ca9dcdb6a5751a58a6160838c6979">
tools/align_benchmark/align_benchmark_params.c
</a>
</li>
<li class="file-stats">
<a href="#f99db7c09eec41dfb7785630b7fae06e9933f932">
tools/align_benchmark/align_benchmark_params.h
</a>
</li>
<li class="file-stats">
<a href="#20d52783ae6ea5c5c01dcce74f1e4fd061d76890">
tools/align_benchmark/benchmark/benchmark_check.c
</a>
</li>
<li class="file-stats">
<a href="#7fb50d8d6900448b7cbd5b0727eaeb04c3a9eb0d">
tools/align_benchmark/benchmark/benchmark_edit.c
</a>
</li>
<li class="file-stats">
<a href="#bfb105101607f59dc57741bb012442bc206ea1db">
tools/align_benchmark/benchmark/benchmark_gap_affine.c
</a>
</li>
<li class="file-stats">
<a href="#57f47db6125923ea109c6621a4461b9a7de2a196">
tools/align_benchmark/benchmark/benchmark_gap_affine2p.c
</a>
</li>
<li class="file-stats">
<a href="#bc9f7dd4284795229b05f09c1e00538f8e0f7a2d">
tools/align_benchmark/benchmark/benchmark_gap_linear.c
</a>
</li>
<li class="file-stats">
<a href="#f1e641165dc1dc5f23292f0efdf19c3ac0c78eb7">
tools/align_benchmark/benchmark/benchmark_indel.c
</a>
</li>
<li class="file-stats">
<a href="#31df983dc1b2a05b67db79547e72def149ceff83">
tools/align_benchmark/benchmark/benchmark_utils.c
</a>
</li>
<li class="file-stats">
<a href="#f7c91514a4b4320b9db216ed9d60d5ec1aa36b52">
tools/align_benchmark/benchmark/benchmark_utils.h
</a>
</li>
<li class="file-stats">
<a href="#40b1f9f420557cff43d06285022c1b479959b194">
tools/align_benchmark/edit/edit_bpm.c
</a>
</li>
<li class="file-stats">
<a href="#77ac2ae2c88921b9dc19241d45e6293f1d4acf6c">
tools/align_benchmark/gap_affine2p/affine2p_matrix.h
</a>
</li>
<li class="file-stats">
<a href="#d970bcc429c6acda7da084af7cdd9aefe2aa55e8">
tools/generate_dataset/generate_dataset.c
</a>
</li>
<li class="file-stats">
<a href="#c1895431d77ad57a0fec1fd73fa6dadbd42b9832">
utils/Makefile
</a>
</li>
<li class="file-stats">
<a href="#ec2fa1f9c07c32da9ee108ee8847f40724a1669e">
utils/commons.h
</a>
</li>
<li class="file-stats">
<a href="#661ebfee41adef32f70ca6565834bcbd813f53e2">
utils/heatmap.h
</a>
</li>
<li class="file-stats">
<a href="#8fff564cf6ab8365bdff94f3e39d08e42e9a18d2">
<span class="deleted-file">

utils/string_padded.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#0086e9fa2bd2ae10cdc77d356a772f09c7864e34">
utils/vector.h
</a>
</li>
<li class="file-stats">
<a href="#602a991ae9625028bd64cf0f0b263d4aaa47f7f7">
wavefront/Makefile
</a>
</li>
<li class="file-stats">
<a href="#d7174bf7985ade97fbdc02cf52d833719a1e78f3">
wavefront/wavefront_align.c
</a>
</li>
<li class="file-stats">
<a href="#e28f97b5026f9693fe9918dc2c7c46326b58cfaa">
wavefront/wavefront_align.h
</a>
</li>
<li class="file-stats">
<a href="#854d667a698ed70f3294192baa8ff053b1e14508">
wavefront/wavefront_aligner.c
</a>
</li>
<li class="file-stats">
<a href="#f98d1f4985b83fa3d2f0dc4dc307b6d4c4720abf">
wavefront/wavefront_aligner.h
</a>
</li>
<li class="file-stats">
<a href="#17b414b45117689898ab1dacdaf906e4c87b7844">
wavefront/wavefront_attributes.c
</a>
</li>
<li class="file-stats">
<a href="#9a585068b941f32415938192a8d7c5f02c304941">
wavefront/wavefront_attributes.h
</a>
</li>
<li class="file-stats">
<a href="#3cb740f1d0083936f1dabbc2c86e81f6dae6f359">
wavefront/wavefront_backtrace.c
</a>
</li>
<li class="file-stats">
<a href="#23d93258af72d63c2997d3a1d3a941cab450cf6d">
wavefront/wavefront_backtrace_buffer.c
</a>
</li>
<li class="file-stats">
<a href="#1f03eea4682456a0c7d2bb35335916e6113e7f53">
wavefront/wavefront_backtrace_buffer.h
</a>
</li>
<li class="file-stats">
<a href="#810118bbeb2b6a004f4566f4bea684bc9428b036">
wavefront/wavefront_backtrace_offload.c
</a>
</li>
<li class="file-stats">
<a href="#ab11492b572e1b7ae65496c988d59c3b05f68e93">
wavefront/wavefront_bialign.c
</a>
</li>
<li class="file-stats">
<a href="#1e3969dbfa72e525ee98dde0bbd7e66d2ea7d4db">
wavefront/wavefront_bialign.h
</a>
</li>
<li class="file-stats">
<a href="#cc26a9c2e656d8a8e43b8beb1471a38db86fc289">
wavefront/wavefront_bialigner.c
</a>
</li>
<li class="file-stats">
<a href="#423d2215b3b463c7167b634487b07635ab05c053">
wavefront/wavefront_bialigner.h
</a>
</li>
<li class="file-stats">
<a href="#938f6f0d8e30f5bdbb61071f5b59fe730eb0258e">
wavefront/wavefront_compute.c
</a>
</li>
<li class="file-stats">
<a href="#d1a27d7e952915e0033dfd77a04e49da4a887c2f">
wavefront/wavefront_compute_affine.c
</a>
</li>
<li class="file-stats">
<a href="#c40861eb7a98c0e646e47619784e9912bb901eff">
wavefront/wavefront_compute_affine2p.c
</a>
</li>
<li class="file-stats">
<a href="#509b8e86a4c1638854c994d0ec799abb16fb20c1">
wavefront/wavefront_compute_edit.c
</a>
</li>
<li class="file-stats">
<a href="#1ec7fc846cea5fe289f6268c63ca4ef7be2b7957">
wavefront/wavefront_compute_linear.c
</a>
</li>
<li class="file-stats">
<a href="#86160c27b782852387e255b161883ca9f357011c">
wavefront/wavefront_debug.c
</a>
</li>
<li class="file-stats">
<a href="#da3e9a1029357dae78d341cb7b18c7f013031d73">
wavefront/wavefront_debug.h
</a>
</li>
<li class="file-stats">
<a href="#d2039c557d1fe4351f599bab0818b2d1ad46f757">
wavefront/wavefront_display.c
</a>
</li>
<li class="file-stats">
<a href="#93a6056363b445a15d4c52c8903fd3ffeaa84553">
wavefront/wavefront_extend.c
</a>
</li>
<li class="file-stats">
<a href="#5d37c97d447aafe9b834f5ea6c0decae54f9a085">
wavefront/wavefront_extend.h
</a>
</li>
<li class="file-stats">
<a href="#0a1ea59fe2941df31dfd7aff542762922148c4c0">
<span class="new-file">
+
wavefront/wavefront_extend_kernels.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#5c7304f0aa272122e4bcd2fe44eb96e9a96bb04e">
<span class="new-file">
+
wavefront/wavefront_extend_kernels.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#5bcc80a48c83f4e2b8f8d5cb94280595804bbaa1">
<span class="new-file">
+
wavefront/wavefront_extend_kernels_avx.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#3e1c8ae347920c8e10f93b133341c96f666a95b7">
<span class="new-file">
+
wavefront/wavefront_extend_kernels_avx.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#55f290d589c38c481be0a86019f1fd653ddcdf3a">
wavefront/wavefront_heuristic.c
</a>
</li>
<li class="file-stats">
<a href="#5ab68cde1c164c12b2e9bfad276d534abff9163c">
wavefront/wavefront_heuristic.h
</a>
</li>
<li class="file-stats">
<a href="#4783ebc288edac59e46d4f1257b36df2b3ae6096">
wavefront/wavefront_offset.h
</a>
</li>
<li class="file-stats">
<a href="#f2d62e8c6b38580f2001529821eca4e85582dbcd">
wavefront/wavefront_pcigar.c
</a>
</li>
<li class="file-stats">
<a href="#af7376582a26d901ef769bc773dc0562f02589c0">
wavefront/wavefront_pcigar.h
</a>
</li>
<li class="file-stats">
<a href="#a50941762a4168d0afc37ef13cdf358dae1b7806">
wavefront/wavefront_penalties.c
</a>
</li>
<li class="file-stats">
<a href="#c52a302b35f4f5b55b57198bcfb657ebcd2d393e">
wavefront/wavefront_penalties.h
</a>
</li>
<li class="file-stats">
<a href="#31db919f9a7722cf0833bfc7044d5355a36831e9">
wavefront/wavefront_plot.c
</a>
</li>
<li class="file-stats">
<a href="#3fbcc6fc6c1b32d88904b768c1a2a78872ced0bf">
wavefront/wavefront_plot.h
</a>
</li>
<li class="file-stats">
<a href="#32ec920e4e69b937a1bb9d9d24f454f882e54332">
<span class="new-file">
+
wavefront/wavefront_sequences.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#dd928b3a8cefd3795a536c85184529b077e9eb7a">
<span class="new-file">
+
wavefront/wavefront_sequences.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#3fd0a7b382cff6ecbef353e0868cc9b5dafa12ea">
<span class="new-file">
+
wavefront/wavefront_termination.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#0c1e19ba24cb9ba4464c475ce052ffe97d0111a9">
<span class="new-file">
+
wavefront/wavefront_termination.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#ee0f6c48490bde5fd6a5303bb226b6f392b71046">
wavefront/wavefront_unialign.c
</a>
</li>
<li class="file-stats">
<a href="#2833c4eafb4a06c0d0f4e051b734cc4f0e8fcf8a">
wavefront/wavefront_unialign.h
</a>
</li>
<li class="file-stats">
<a href="#72da42be38605d31d63603f3d1fff54f5256e08d">
wavefront/wfa.h
</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>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #626168;">

<br>
<a href="https://salsa.debian.org/med-team/libwfa2/-/commit/89967301d3c6930b9ed04a313e31929d13cc1ddb">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>
<span style="color: transparent; font-size: 0; display: none; overflow: hidden; opacity: 0; width: 0; height: 0; max-width: 0; max-height: 0;">
Notification message regarding https://salsa.debian.org/med-team/libwfa2/-/commit/89967301d3c6930b9ed04a313e31929d13cc1ddb at 1777612700
</span>
<script type="application/ld+json">{"@context":"http://schema.org","@type":"EmailMessage","action":{"@type":"ViewAction","name":"View Commit","url":"https://salsa.debian.org/med-team/libwfa2/-/commit/89967301d3c6930b9ed04a313e31929d13cc1ddb"}}</script>


</p>
</div>
</body>
</html>