<!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;">
Pierre Gruet pushed to branch upstream at <a href="https://salsa.debian.org/med-team/picard-tools">Debian Med / picard-tools</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/picard-tools/-/commit/9e6fceda1939d1e7f0065577e787e70639d13591">9e6fceda</a></strong>
<div>
<span> by Pierre Gruet </span> <i> at 2025-12-23T15:28:49+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; 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 3.4.0+dfsg</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
31 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#da79ec0a668f7046c8dcfb73c8e1670a3426c431">
.github/workflows/cloud_tests.yml
</a>
</li>
<li class="file-stats">
<a href="#6b8eb1151e11abd72b31ffb764de06790e5bda1e">
.github/workflows/tests.yml
</a>
</li>
<li class="file-stats">
<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
</a>
</li>
<li class="file-stats">
<a href="#762af087b77f49609f8894513a9626fc339c8ff5">
<span class="new-file">
+
src/main/java/picard/analysis/CollectUmiPrevalenceMetrics.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#10622eebc55d531a6d58705fbdd3b8f4ca95b439">
src/main/java/picard/analysis/directed/HsMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#6709bebe3eda7862090b4368f85682e749a0f58a">
src/main/java/picard/arrays/CreateVerifyIDIntensityContaminationMetricsFile.java
</a>
</li>
<li class="file-stats">
<a href="#33b117cf97b036a70b756207fe271314700659bd">
<span class="new-file">
+
src/main/java/picard/filter/CountingFilterWrapper.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#d14447f9485eb95d9cb9fe02e081a47cf64d74bc">
src/main/java/picard/fingerprint/CalculateFingerprintMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#4b494ef67355a05286058b71311a9448ce743651">
src/main/java/picard/fingerprint/CheckFingerprint.java
</a>
</li>
<li class="file-stats">
<a href="#f7d76d352dfb807611c35d4412191ed995aa7003">
src/main/java/picard/fingerprint/CrosscheckFingerprints.java
</a>
</li>
<li class="file-stats">
<a href="#c3522ad5b834cc5c5ba705bd1f56a4c19c5c6348">
src/main/java/picard/fingerprint/ExtractFingerprint.java
</a>
</li>
<li class="file-stats">
<a href="#b8553f759ce8bc72a7ed6f6994097c2fc323b375">
src/main/java/picard/fingerprint/FingerprintChecker.java
</a>
</li>
<li class="file-stats">
<a href="#785cd63b1416a086e5bb4a3119c81f45982e6d46">
src/main/java/picard/fingerprint/FingerprintUtils.java
</a>
</li>
<li class="file-stats">
<a href="#6e409513cd0a557c059cfde172d84ac259871fbe">
src/main/java/picard/fingerprint/IdentifyContaminant.java
</a>
</li>
<li class="file-stats">
<a href="#ccbdc441f0476e940c3ee8a63395e8f9e08a755f">
src/main/java/picard/fingerprint/Snp.java
</a>
</li>
<li class="file-stats">
<a href="#0aa89b8f8e77671c55913bf020ceca341bd6ce20">
src/main/java/picard/sam/SamComparisonMetric.java
</a>
</li>
<li class="file-stats">
<a href="#3c197fbee6fa21f3f4690a489c2afc942ee7d096">
src/main/java/picard/sam/SamErrorMetric/SimpleErrorCalculator.java
</a>
</li>
<li class="file-stats">
<a href="#61a4238b24579fdfac2bacdffc5bc57b36b76d92">
src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java
</a>
</li>
<li class="file-stats">
<a href="#27b373658b0266838a2e7b5abf9e09f5c4da3488">
src/main/java/picard/sam/markduplicates/MarkDuplicates.java
</a>
</li>
<li class="file-stats">
<a href="#5fa8369d80f10e43b11ba9e72097baeccdd86ebe">
src/main/java/picard/sam/util/SamComparison.java
</a>
</li>
<li class="file-stats">
<a href="#6d29efa301dfe7d55a00774547f4cf67aea4ef28">
src/main/java/picard/util/SequenceDictionaryUtils.java
</a>
</li>
<li class="file-stats">
<a href="#b339df8c33c878526b4a12b9dc93fc258e74673a">
src/main/java/picard/vcf/MergeVcfs.java
</a>
</li>
<li class="file-stats">
<a href="#af829796a2fa3338636847a97270783f268114ba">
<span class="new-file">
+
src/test/java/picard/analysis/CollectUmiPrevalenceMetricsTest.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#6dac1c7c1b4d9022ddd3bc5f57a44bb077b0983c">
src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
</a>
</li>
<li class="file-stats">
<a href="#acb164f6acc53f017a0420c96f54cf5b32e23d47">
src/test/java/picard/fingerprint/CheckFingerprintTest.java
</a>
</li>
<li class="file-stats">
<a href="#8e47b09e231ce09b8b2b713f2020679c7cc00327">
src/test/java/picard/fingerprint/FingerprintCheckerTest.java
</a>
</li>
<li class="file-stats">
<a href="#c943745ef09ac1f0ccca685978e8147e2cc93cd7">
src/test/java/picard/sam/SamErrorMetric/BaseErrorCalculationTest.java
</a>
</li>
<li class="file-stats">
<a href="#f5dc81fafe32fa8c26317f0f7de65d3ce459aa32">
src/test/java/picard/sam/SamErrorMetric/CollectSamErrorMetricsTest.java
</a>
</li>
<li class="file-stats">
<a href="#2fd9722ae2599d1b5b328e86dcad1751912317e7">
src/test/java/picard/sam/util/SamComparisonTest.java
</a>
</li>
<li class="file-stats">
<a href="#93430aaf834673041a584bcd12b6da0282ce251f">
<span class="new-file">
+
testdata/picard/independent_replicates/twopairsWithManyUmis.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#cc5f57e929ac3208f9159916b055eb0017b2f975">
testdata/picard/reference/chrM.reference.fasta
</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/picard-tools/-/commit/9e6fceda1939d1e7f0065577e787e70639d13591">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/picard-tools/-/commit/9e6fceda1939d1e7f0065577e787e70639d13591 at 1766742766
</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/picard-tools/-/commit/9e6fceda1939d1e7f0065577e787e70639d13591"}}</script>
</p>
</div>
</body>
</html>