<!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;">
Pierre Gruet pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/picard-tools" style="color: #1068bf;">Debian Med / picard-tools</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/picard-tools/-/commit/f17ae3a5adf9516c80a4e5d57455fa80fe172c0f" style="color: #1068bf;">f17ae3a5</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-09-22T16:29:27+02:00</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 2.27.4+dfsg</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302" style="color: #1068bf;">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#f07866736216be0ee2aba49e392191aeae700a35" style="color: #1068bf;">
build.gradle
</a>
</li>
<li class="file-stats">
<a href="#bac4c9ac8d5063b8b48c84e1a30915ee1d4b4523" style="color: #1068bf;">
src/main/java/picard/analysis/AlignmentSummaryMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#39ad2a42470243aa1402488d16e8309995fc1180" style="color: #1068bf;">
src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
</a>
</li>
<li class="file-stats">
<a href="#b2834490f63ed514ea04878a07bfeb9a3745de6c" style="color: #1068bf;">
src/main/java/picard/analysis/CollectQualityYieldMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#04f554de73499a24d9a36adee63d01f42eabc54c" style="color: #1068bf;">
<span class="new-file">
+
src/main/java/picard/analysis/HistogramGenerator.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#da9ff87ef6c58326bf722021f76a9882a5eea09c" style="color: #1068bf;">
src/main/java/picard/analysis/MeanQualityByCycle.java
</a>
</li>
<li class="file-stats">
<a href="#7882db8ab241e139efe87ded3c26da9c35a5cb4e" style="color: #1068bf;">
src/main/java/picard/sam/DuplicationMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#55f29fe36334314691ce337d64ef345df3080488" style="color: #1068bf;">
<span class="new-file">
+
src/main/java/picard/sam/DuplicationMetricsFactory.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#84b122487bdf3fa3944ce73212d3af977f5deb46" style="color: #1068bf;">
src/main/java/picard/sam/FastqToSam.java
</a>
</li>
<li class="file-stats">
<a href="#e568abd8f2178d5253a0066ddb4cbe7cb5bafa7c" style="color: #1068bf;">
<span class="new-file">
+
src/main/java/picard/sam/FlowBasedDuplicationMetrics.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#735eb3dc422ffa57ecb5c1e5b501aede2eb827b6" style="color: #1068bf;">
src/main/java/picard/sam/RevertSam.java
</a>
</li>
<li class="file-stats">
<a href="#2120d65da84b4b7a5d51519d03bd830e009237d7" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/CollectDuplicateMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#61a4238b24579fdfac2bacdffc5bc57b36b76d92" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java
</a>
</li>
<li class="file-stats">
<a href="#27b373658b0266838a2e7b5abf9e09f5c4da3488" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/MarkDuplicates.java
</a>
</li>
<li class="file-stats">
<a href="#302bd3c48e0da54a59efdd3b7e0d9ed951e87788" style="color: #1068bf;">
<span class="new-file">
+
src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowArgumentCollection.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc5a860aef8f6e090b2931763dca28f71e409fc1" style="color: #1068bf;">
<span class="new-file">
+
src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowHelper.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#4daa9c46e506cfddef42ff59eee398f8ec61aacc" style="color: #1068bf;">
<span class="new-file">
+
src/main/java/picard/sam/markduplicates/MarkDuplicatesHelper.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#fff827ed4284ba3f43bdc37f22b6b82d83c2d2e2" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/MarkDuplicatesWithMateCigarIterator.java
</a>
</li>
<li class="file-stats">
<a href="#8ad686c82529eba8ecafc5adb5e9abf298d598cc" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/SimpleMarkDuplicatesWithMateCigar.java
</a>
</li>
<li class="file-stats">
<a href="#29126ce694b74453b952ea35f1defd61b5dc1b83" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java
</a>
</li>
<li class="file-stats">
<a href="#cf498877f67ccdc131c3b4a9aaa43351b05b4275" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/util/LibraryIdGenerator.java
</a>
</li>
<li class="file-stats">
<a href="#0a053fb38482a12b21fb9d58286462f0ab7fc52a" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/util/ReadEnds.java
</a>
</li>
<li class="file-stats">
<a href="#817026c0d3e01126ec550ed4203b147e4878d567" style="color: #1068bf;">
src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicates.java
</a>
</li>
<li class="file-stats">
<a href="#75a0dd1ada68fe38e3364986eac314d03a853bfd" style="color: #1068bf;">
src/main/java/picard/util/AccumulateQualityYieldMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#9226c9f283cb687d49cfd9e0a4d46fa83d39b803" style="color: #1068bf;">
src/main/java/picard/vcf/GenotypeConcordance.java
</a>
</li>
<li class="file-stats">
<a href="#f519c039d1aa31afafc4e8d00dca3190aeac1f21" style="color: #1068bf;">
src/test/java/picard/analysis/CollectQualityYieldMetricsTest.java
</a>
</li>
<li class="file-stats">
<a href="#2fd364663723790d1032a20b6431f11595ce86b7" style="color: #1068bf;">
src/test/java/picard/sam/CramCompatibilityTest.java
</a>
</li>
<li class="file-stats">
<a href="#a13eae93f83bfa8c9c692e0760f3b181227f2192" style="color: #1068bf;">
src/test/java/picard/sam/DuplicationMetricsTest.java
</a>
</li>
<li class="file-stats">
<a href="#cb5d08b6bf534cfa0b86115ccdbaae6c49f640ca" style="color: #1068bf;">
src/test/java/picard/sam/FastqToSamTest.java
</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/picard-tools/-/commit/f17ae3a5adf9516c80a4e5d57455fa80fe172c0f" 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>
<script type="application/ld+json">{"@context":"http://schema.org","@type":"EmailMessage","action":{"@type":"ViewAction","name":"View Commit","url":"https://salsa.debian.org/med-team/picard-tools/-/commit/f17ae3a5adf9516c80a4e5d57455fa80fe172c0f"}}</script>
</p>
</div>
</body>
</html>