<!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=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: .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;">
Dylan Aïssi pushed to branch upstream at <a href="https://salsa.debian.org/med-team/beagle">Debian Med / beagle</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/beagle/-/commit/64cf178bc1d96c6fe27580547b319e466a167a27">64cf178b</a></strong>
<div>
<span> by Dylan Aïssi </span> <i> at 2025-02-03T22:45:17+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; 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 241217</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#82ed8855da81abac877dbd07e4faa17b2774a3fd">
beagleutil/CompHapSegment.java
</a>
</li>
<li class="file-stats">
<a href="#a4bc486b85abac7297ff55f6cdea725aa089711c">
blbutil/BitArray.java
</a>
</li>
<li class="file-stats">
<a href="#0cf2c85c588a2fb59c97c97c485cc8a66f5a0f53">
blbutil/BlockLineReader.java
</a>
</li>
<li class="file-stats">
<a href="#cde7bd63ffdb333806d832fd9b3c91737660465d">
blbutil/FileIt.java
</a>
</li>
<li class="file-stats">
<a href="#6079b16bd032367aafb4fb3b5a7ec3cc428ebc03">
blbutil/FileUtil.java
</a>
</li>
<li class="file-stats">
<a href="#1928aebe75a42243fe3f56cf57a32c12bb414d3e">
blbutil/InputIt.java
</a>
</li>
<li class="file-stats">
<a href="#7a798522c1cf1af1069d4ed6e51d61b403f767d8">
<span class="new-file">
+
blbutil/TriFunction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#569d1e1ae30f252e98526e6aa870ed406131b290">
blbutil/Utilities.java
</a>
</li>
<li class="file-stats">
<a href="#b2ba9080612250531e5601745e2e52ed48f1770e">
bref/AsIsBref3Writer.java
</a>
</li>
<li class="file-stats">
<a href="#88c53e80182ef20a8cdfed427d5e651d37907e75">
bref/Bref3.java
</a>
</li>
<li class="file-stats">
<a href="#7115a9be428f9d40e14bb3bcde8291e77725fef1">
<span class="new-file">
+
bref/Bref3Header.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#75b4875e136736cf8fa3756993e43d51ba5a980f">
bref/Bref3It.java
</a>
</li>
<li class="file-stats">
<a href="#923ab2081306a60ce903c2304d7d5d6f3224175c">
bref/Bref3Reader.java
</a>
</li>
<li class="file-stats">
<a href="#235afaa37fdb61b1d835aad391a3b55eb608864e">
bref/CompressBref3Writer.java
</a>
</li>
<li class="file-stats">
<a href="#8858d04c3e071f8148d52b04a39944b5f4560a7a">
bref/SeqCoder3.java
</a>
</li>
<li class="file-stats">
<a href="#dcb0e12a67291331c7d1fd8dd651714b291527c8">
bref/UnBref3.java
</a>
</li>
<li class="file-stats">
<a href="#315086b42467cd64d67b45236c874d197c068244">
imp/ImpStates.java
</a>
</li>
<li class="file-stats">
<a href="#156b60cc697d7e2105fc5f6116490daeacee2f47">
imp/ImputedRecBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#c41b3596551b934f865399c65e791fb8ddce7828">
ints/PackedIntArray.java
</a>
</li>
<li class="file-stats">
<a href="#f70826f4cf6c50e09c6eda07a4245a5e2f83efb8">
ints/UnsignedByteArray.java
</a>
</li>
<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
</a>
</li>
<li class="file-stats">
<a href="#eb9d1a1acbc4ec0ffa4eeee52a6d83ce5c15c2e1">
main/Par.java
</a>
</li>
<li class="file-stats">
<a href="#611062e8e142f9ef1d5f5200bb13b0a16611898e">
main/RunStats.java
</a>
</li>
<li class="file-stats">
<a href="#5cd7995a7684c4895d668ddb8873a9fba68706d1">
main/WindowWriter.java
</a>
</li>
<li class="file-stats">
<a href="#b1d7cb2db18d084fa285491c1742e35ce2f12f43">
phase/BasicPhaseStates.java
</a>
</li>
<li class="file-stats">
<a href="#07777d8f0265190c58c0ca3fad4559f401a7fd13">
phase/FixedPhaseData.java
</a>
</li>
<li class="file-stats">
<a href="#048375da7caf8dfaca0cc1a787bea46ec68c6f9e">
phase/FwdPbwtPhaser.java
</a>
</li>
<li class="file-stats">
<a href="#8d85139a044149b6a2dee62e1ed355e1a107e93a">
phase/HmmUpdater.java
</a>
</li>
<li class="file-stats">
<a href="#bff5675255d46d340fc57b49cdb9d933b6ba9ad4">
phase/Ibs2.java
</a>
</li>
<li class="file-stats">
<a href="#116f5d3033760c490b9f24d2407d7fb009978f22">
phase/Ibs2Sets.java
</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: #737278;">
—
<br>
<a href="https://salsa.debian.org/med-team/beagle/-/commit/64cf178bc1d96c6fe27580547b319e466a167a27">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>
<script type="application/ld+json">{"@context":"http://schema.org","@type":"EmailMessage","action":{"@type":"ViewAction","name":"View Commit","url":"https://salsa.debian.org/med-team/beagle/-/commit/64cf178bc1d96c6fe27580547b319e466a167a27"}}</script>
</p>
</div>
</body>
</html>