<!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, "Menlo"), DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<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: var(--default-regular-font, -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: var(--default-regular-font, -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 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: bold;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/b09c2300c9285459cd67ebe93f37f246694d7487">b09c2300</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2023-02-20T14:07:02+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/7407ab1103471a1e9511c616adfc33d225c323ac">7407ab11</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2023-02-20T14:07:03+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.1.2</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/d7ea31fae9bc842f228e9ca24c357ade9aa7e742">d7ea31fa</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2023-02-20T14:07:08+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/2.1.2'

Update to upstream version '2.1.2'
with Debian dir a47d5d085872511a935eb7dae447fcdb03eff811</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/b7d263f06ab9370e927ef9a8a0c77cbff8c8ce7c">b7d263f0</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2023-02-20T14:07:27+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: #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: bold;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/628b5e8acbdd585f4be1ea870f4dee02f056eb5b">628b5e8a</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2023-02-23T17:30:48+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/065126df252d16dc506e92f55f51b80a6dbf0303">065126df</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2023-02-23T17:30:50+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2.1.3</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/8c563cfb5672ce96f4fad659ed29da21dda25fdb">8c563cfb</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2023-02-23T17:30:53+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/2.1.3'

Update to upstream version '2.1.3'
with Debian dir 56ab10cf4d074ba833f128be6a7e3637ce988b91</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/diamond-aligner/-/commit/4f42257f53d6490da5d2ecc2447244be6b649dd6">4f42257f</a></strong>
<div>
<span> by Michael R. Crusoe </span> <i> at 2023-02-23T18:47:39+01:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "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: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#c7fe42138e1c33a6d76bbf9a03822d41e03da2cc">
<span class="new-file">
+
.cirrus.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#9ae3f8f5993cde39520379ad6054df829e6c91a7">
.github/workflows/cmake.yml
</a>
</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">
<span class="new-file">
+
azure-pipelines.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#ba308c53c268704c3008f5e2e6e8129f9f6bf3fe">
src/ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#f76380e3e66f9453de89e5ac198478544cf1e6e4">
src/align/align.cpp
</a>
</li>
<li class="file-stats">
<a href="#f1fae2471d3aa9a609a9966be5b7ab4c0f58fa75">
src/align/align.h
</a>
</li>
<li class="file-stats">
<a href="#8310f6d8c536d182ebd128c5e462f7c6addcbf6d">
src/align/culling.cpp
</a>
</li>
<li class="file-stats">
<a href="#5a2381540b8362260dcaa6747086bb358097256e">
src/align/extend.cpp
</a>
</li>
<li class="file-stats">
<a href="#9fc8681bb50d867858382e8ecdfd9bc32570af85">
src/align/gapped_final.cpp
</a>
</li>
<li class="file-stats">
<a href="#7540abd0721601ec3b35ecdd671f39ce63cef20f">
src/align/gapped_score.cpp
</a>
</li>
<li class="file-stats">
<a href="#1b90f5ee8b6ca86e42623b99dcbd74ad0880c831">
src/align/global_ranking/global_ranking.cpp
</a>
</li>
<li class="file-stats">
<a href="#8f9453cefaa66bad075c8bcb49a08b740b24e222">
src/align/legacy/banded_swipe_pipeline.cpp
</a>
</li>
<li class="file-stats">
<a href="#b2abd29d918a248e9564e135672e01b243a8ee3a">
<span class="new-file">
+
src/align/legacy/pipeline.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#0b08202a0e53b77834bad522a650ac3fd069ede6">
src/align/load_hits.h
</a>
</li>
<li class="file-stats">
<a href="#76d5a97c09cca591280144de40f9c04a5ec57ef7">
src/basic/basic.cpp
</a>
</li>
<li class="file-stats">
<a href="#fe8c534c15ea9cf93547993244c3ab903c4895ff">
src/basic/config.cpp
</a>
</li>
<li class="file-stats">
<a href="#79a175a8b141cc4f06683108fcd39b79a555f1cd">
src/basic/config.h
</a>
</li>
<li class="file-stats">
<a href="#da280a51d91809345347036c4e31920b2c744ab7">
src/basic/const.h
</a>
</li>
<li class="file-stats">
<a href="#f9492756ecc3a6486c8d8a74972ab3c60ae604a2">
src/basic/match.h
</a>
</li>
<li class="file-stats">
<a href="#843b0c321950eaab30ec044ec3ceb34583b31189">
src/cluster/cascaded/cascaded.cpp
</a>
</li>
<li class="file-stats">
<a href="#6444af7c027138203099756fde20af9fa7cae118">
src/cluster/cascaded/cascaded.h
</a>
</li>
<li class="file-stats">
<a href="#afd2efeccfbb0d08402b8781faab7a8e3500da7c">
src/cluster/cascaded/helpers.cpp
</a>
</li>
<li class="file-stats">
<a href="#58d7c1b60192f25ddb57682da626d8207f8b0cf9">
src/cluster/cascaded/recluster.cpp
</a>
</li>
<li class="file-stats">
<a href="#5bc1484cf89972fcb12a4416856680fe6ec184a1">
src/cluster/cascaded/wrapper.cpp
</a>
</li>
<li class="file-stats">
<a href="#e32575ef2e63f2a583912aa5a951281d34cc36fb">
src/cluster/helpers.cpp
</a>
</li>
<li class="file-stats">
<a href="#5ade76184f5f0172ca86104f68fb1af124446f8c">
src/cluster/output.cpp
</a>
</li>
<li class="file-stats">
<a href="#ed0f43ddafbd5bf4b786d583b7e939448d6496ba">
src/cluster/realign.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: #737278;">

<br>
<a href="https://salsa.debian.org/med-team/diamond-aligner/-/compare/c39c9c29d29de2449048284b276e4d425a0c8c21...4f42257f53d6490da5d2ecc2447244be6b649dd6">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>



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