<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en">
<head>
<meta content="text/html; charset=US-ASCII" 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: 0.875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,0.01) 0 0 1px;
}
body {
font-family: -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(255,255,255,0.01) 0 0 1px; font-family: -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;">
Andreas Tille pushed to branch master at <a href="https://salsa.debian.org/med-team/bowtie2" style="color: #1068bf;">Debian Med / bowtie2</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/ae6f1ec6c1f507dc85b889369ca9929664dbd087" style="color: #1068bf;">ae6f1ec6</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-11-04T19:56:13+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 2.5.0</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/9dde506457a3f54b4ac662f281402cfa468f6bf4" style="color: #1068bf;">9dde5064</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-11-04T19:56:13+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/9809cd92dacb41ab80cbad1c4510f900d53be26b" style="color: #1068bf;">9809cd92</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-11-04T19:56:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Update upstream source from tag 'upstream/2.5.0'
Update to upstream version '2.5.0'
with Debian dir d43192418f3164832e48405c9da89906f697677b</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/72ee06d4cc122ca26948402f408c356fd42637df" style="color: #1068bf;">72ee06d4</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-11-04T19:56:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>routine-update: Standards-Version: 4.6.1
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/e4f5b10245db8cd9d082479b78d90996fb37c49c" style="color: #1068bf;">e4f5b102</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-11-04T19:56:33+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/c9b4d7a6b7b79071925033a5806105660babee59" style="color: #1068bf;">c9b4d7a6</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-11-04T19:56:38+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Set upstream metadata fields: Bug-Database.
Changes-By: lintian-brush
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/bowtie2/-/commit/f90758ae2ac89e8a02573fac45062a524a5ea5c0" style="color: #1068bf;">f90758ae</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2022-11-04T20:15:46+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>Update patches
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
18 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#32e7b86fef2d14e50d14716af4894aac7779f716" style="color: #1068bf;">
<span class="new-file">
+
.github/workflows/random-tests.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#7a37717622fd6c0538b1b8776cdd4e30d3a990c8" style="color: #1068bf;">
.github/workflows/bowtie2.yml
→
.github/workflows/simple-tests.yml
</a>
</li>
<li class="file-stats">
<a href="#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44" style="color: #1068bf;">
.gitmodules
</a>
</li>
<li class="file-stats">
<a href="#dea7d9d2c0ed0c505374f9f90877bedd8f077710" style="color: #1068bf;">
BOWTIE2_VERSION
</a>
</li>
<li class="file-stats">
<a href="#f11fb3bba37e7060bedcd5895812b7c511c52651" style="color: #1068bf;">
MANUAL
</a>
</li>
<li class="file-stats">
<a href="#465370da702349b6dcb3f9f2026872cad6877efa" style="color: #1068bf;">
MANUAL.markdown
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c" style="color: #1068bf;">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8" style="color: #1068bf;">
NEWS
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d" style="color: #1068bf;">
README.md
</a>
</li>
<li class="file-stats">
<a href="#ba2785396de3010a0336f821fda40b4992ec9409" style="color: #1068bf;">
aligner_bt.cpp
</a>
</li>
<li class="file-stats">
<a href="#d0b93e802a57a9f254ad87c9890869508854e2e3" style="color: #1068bf;">
aligner_cache.h
</a>
</li>
<li class="file-stats">
<a href="#a177c5447e9cdcbfd7d1dc1c7140293d0cfbc779" style="color: #1068bf;">
aligner_seed.cpp
</a>
</li>
<li class="file-stats">
<a href="#c9b466ab26199558112972a17a75b8c21ac85c19" style="color: #1068bf;">
aligner_seed.h
</a>
</li>
<li class="file-stats">
<a href="#9b9c3e8e49dbc147620bdc9c0e3d970e5ee41ea9" style="color: #1068bf;">
aligner_sw_driver.cpp
</a>
</li>
<li class="file-stats">
<a href="#ebe4860ccf0cdb1c657efaf27d61b77c8bc884e0" style="color: #1068bf;">
aligner_swsse.cpp
</a>
</li>
<li class="file-stats">
<a href="#e32a224a6267047bc87591ba748a30ebf008f885" style="color: #1068bf;">
aligner_swsse.h
</a>
</li>
<li class="file-stats">
<a href="#3e59afb96cc7e4287aebc91552bc0739a389667d" style="color: #1068bf;">
aligner_swsse_ee_i16.cpp
</a>
</li>
<li class="file-stats">
<a href="#db01803ecfdff4ed1bbcf3e3443f63b68e3f1772" style="color: #1068bf;">
aligner_swsse_ee_u8.cpp
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">
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: #666;">
—
<br>
<a href="https://salsa.debian.org/med-team/bowtie2/-/compare/18286445c6a460af79361adfdd6d8ad22811a15c...f90758ae2ac89e8a02573fac45062a524a5ea5c0" style="color: #1068bf;">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" style="color: #1068bf;">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link" style="color: #1068bf;">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link" style="color: #1068bf;">Help</a>
</p>
</div>
</body>
</html>