<!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>img {
max-width: 100%; height: auto;
}
</style>
</head>
<body>
<div class="content">
<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/picard-tools">Debian Med / picard-tools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/beb54d3cf2a3541c5990e91f76b251f5545b72fc">beb54d3c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-08-27T17:06:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.23.3+dfsg</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
</a>
</li>
<li class="file-stats">
<a href="#2269f0b41b877093e5ef84c96198be511137ddbc">
src/main/java/picard/analysis/CollectMultipleMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#aeb3cb9c88748b54a0beea66707d8c4b0507be57">
src/main/java/picard/arrays/ArraysCallingMetricAccumulator.java
</a>
</li>
<li class="file-stats">
<a href="#cf132dbe9e717d8c260a4178d5b64adf408c06cc">
src/main/java/picard/arrays/CollectArraysVariantCallingMetrics.java
</a>
</li>
<li class="file-stats">
<a href="#df4dc620efcebfaf5b5242aaf6701781c854f842">
src/main/java/picard/arrays/CombineGenotypingArrayVcfs.java
</a>
</li>
<li class="file-stats">
<a href="#f91c189fd4550d2b3a19984cf8214fc36e993efb">
src/main/java/picard/arrays/GtcToVcf.java
</a>
</li>
<li class="file-stats">
<a href="#d71a309d7e87d38051648d80540afcffb9dff561">
<span class="new-file">
+
src/main/java/picard/arrays/illumina/BpmToNormalizationManifestCsv.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#14bf942877365386019fca7216d550be88788d09">
src/main/java/picard/arrays/illumina/CompareGtcFiles.java
</a>
</li>
<li class="file-stats">
<a href="#a96221eeb7972c91f16503644debfa6080aa98e9">
<span class="new-file">
+
src/main/java/picard/arrays/illumina/IlluminaBPMFile.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#2153898b667a816a34fd89fa93fa2047d3b85547">
<span class="new-file">
+
src/main/java/picard/arrays/illumina/IlluminaBPMLocusEntry.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#5cc86ec2adb7e484276793b9e78d120178ebdc9b">
src/main/java/picard/arrays/illumina/InfiniumDataFile.java
</a>
</li>
<li class="file-stats">
<a href="#63b8e622485f24ca7d415bd6b664d8945f37f285">
src/main/java/picard/arrays/illumina/InfiniumEGTFile.java
</a>
</li>
<li class="file-stats">
<a href="#ba0b62634fb0a7a59ef3fd636dc30c32065b15a7">
src/main/java/picard/arrays/illumina/InfiniumGTCFile.java
</a>
</li>
<li class="file-stats">
<a href="#b9b651583fcedc46139b545c2a6e6885e7f47f80">
src/main/java/picard/arrays/illumina/InfiniumVcfFields.java
</a>
</li>
<li class="file-stats">
<a href="#1fa2570ced8b3c33e4b3bd1f563ab3786ec64e29">
src/main/java/picard/cmdline/CommandLineProgram.java
</a>
</li>
<li class="file-stats">
<a href="#86ac663cd55856855f703ea436ae922385440eff">
<span class="new-file">
+
src/main/java/picard/fingerprint/CappedHaplotypeProbabilities.java
</span>
</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">
<span class="new-file">
+
src/main/java/picard/fingerprint/ExtractFingerprint.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#2610eeec16f86a2981df3a83c90f157d64b1a639">
src/main/java/picard/fingerprint/Fingerprint.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="#b004cfac2a9f021fc9d1b4ec81c773be3e52bf85">
src/main/java/picard/fingerprint/HaplotypeProbabilitiesFromContaminatorSequence.java
</a>
</li>
<li class="file-stats">
<a href="#094367444643af389daf8205b9941bab6c327a03">
src/main/java/picard/fingerprint/HaplotypeProbabilitiesUsingLogLikelihoods.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="#2168b1a85a272cff25cf756eb8949f5a5f2b1cfa">
<span class="new-file">
+
src/main/java/picard/fingerprint/LiftOverHaplotypeMap.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#fe1d7e19bc6106746788f35fe5d764e5009ab355">
src/main/java/picard/fingerprint/MatchResults.java
</a>
</li>
<li class="file-stats">
<a href="#053dfd8dba5135bfe7b20c2ce7ce296f5829a06c">
src/main/java/picard/sam/CreateSequenceDictionary.java
</a>
</li>
<li class="file-stats">
<a href="#24597f37909f2f46c79e31b9aced5c95eaf26241">
src/main/java/picard/sam/MergeBamAlignment.java
</a>
</li>
<li class="file-stats">
<a href="#3c276b3c14fcc3d9d792d86ca7609a8a0b52ba6f">
<span class="new-file">
+
src/main/java/picard/sam/markduplicates/CheckDuplicateMarking.java
</span>
</a>
</li>
</ul>
<h5>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: #777;">
—
<br>
<a href="https://salsa.debian.org/med-team/picard-tools/-/commit/beb54d3cf2a3541c5990e91f76b251f5545b72fc">View it on GitLab</a>.
<br>
You're receiving this email because of your account on salsa.debian.org.
If you'd like to receive fewer emails, you can
adjust your notification settings.
<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/beb54d3cf2a3541c5990e91f76b251f5545b72fc"}}</script>
</p>
</div>
</body>
</html>