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<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>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/0601fb2b9891fdbcabec88cd48b338fdb88a805d">0601fb2b</a></strong>
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<span> by Pierre Gruet </span> <i> at 2024-12-05T12:35:41+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #28272d; 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 3.3.0+dfsg</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
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<a href="#da79ec0a668f7046c8dcfb73c8e1670a3426c431">
.github/workflows/cloud_tests.yml
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<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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<a href="#f07866736216be0ee2aba49e392191aeae700a35">
build.gradle
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<a href="#6909ff640be7be2de90d276c91938e5bcd21a003">
build_push_docker.sh
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<a href="#fbe448ebfc3eb2d4e308f6b8b043666f5b57235e">
gradle/wrapper/gradle-wrapper.properties
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<a href="#5bbfa66edb4db3c7c33c5181f43510990d3307f9">
gradlew
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<a href="#b2834490f63ed514ea04878a07bfeb9a3745de6c">
src/main/java/picard/analysis/CollectQualityYieldMetrics.java
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src/main/java/picard/analysis/CollectQualityYieldMetricsFlow.java
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src/main/java/picard/analysis/CollectQualityYieldMetricsSNVQ.java
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<a href="#a4eadc1086ad98cf8ee663d0279108246675300e">
src/main/java/picard/analysis/directed/PanelMetricsBase.java
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<a href="#7dc078e8a631cb6833fea5fe97f4d605fadaef7f">
src/main/java/picard/analysis/directed/TargetMetricsCollector.java
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<a href="#1fa2570ced8b3c33e4b3bd1f563ab3786ec64e29">
src/main/java/picard/cmdline/CommandLineProgram.java
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<a href="#e3b3b1cd9be6d534484fdcd4ab194e2b5e8c63cc">
src/main/java/picard/cmdline/StandardOptionDefinitions.java
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<a href="#9e7687ac48dd3a58cfe1116ec1766bbe72495f19">
src/main/java/picard/cmdline/argumentcollections/OptionalReferenceArgumentCollection.java
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<a href="#64b06edd6c9e122bd332f42f569ea625fcb0c8e2">
src/main/java/picard/cmdline/argumentcollections/ReferenceArgumentCollection.java
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<a href="#6e6411518c7f76b82896b93ba22e44787d100789">
src/main/java/picard/cmdline/argumentcollections/RequiredReferenceArgumentCollection.java
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<a href="#b8553f759ce8bc72a7ed6f6994097c2fc323b375">
src/main/java/picard/fingerprint/FingerprintChecker.java
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<a href="#ff081ec7e7b341ec15cdfe57e1845837d4ed5168">
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src/main/java/picard/flow/FlowBasedArgumentCollection.java
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src/main/java/picard/flow/FlowBasedKeyCodec.java
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src/main/java/picard/flow/FlowBasedRead.java
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src/main/java/picard/flow/FlowReadGroupInfo.java
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<a href="#0e4df388a5a1a3a9007b3729d94765d3d2911e23">
src/main/java/picard/nio/DeleteRecursive.java
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<a href="#f3be9820e36304c921110234714f5ef95cbf8b09">
src/main/java/picard/nio/GATKBucketUtils.java
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src/main/java/picard/nio/PicardBucketUtils.java
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<a href="#4e2c4310035e6fccac7e52a1d6f396200cfb0658">
src/main/java/picard/nio/PicardHtsPath.java
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<a href="#af2a56413fca14e72376e746c012773ef875b597">
src/main/java/picard/nio/GATKIOUtils.java
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src/main/java/picard/nio/PicardIOUtils.java
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<a href="#87cdeb4d4b2d5d5f8a0e9c7a523936565c36e141">
src/main/java/picard/sam/AbstractAlignmentMerger.java
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<a href="#053dfd8dba5135bfe7b20c2ce7ce296f5829a06c">
src/main/java/picard/sam/CreateSequenceDictionary.java
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<a href="#d7e1eb1d5142d7f5e0ed5760254a640075f59bc3">
src/main/java/picard/sam/DownsampleSam.java
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<li class="file-stats">
<a href="#24597f37909f2f46c79e31b9aced5c95eaf26241">
src/main/java/picard/sam/MergeBamAlignment.java
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<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
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