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<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>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/ac518bb5f410586638e4af3f2a8c885ac740b525" style="color: #1068bf;">ac518bb5</a></strong>
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<span> by Pierre Gruet </span> <i> at 2022-11-01T20:28:47+01:00 </i>
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<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 2.27.5+dfsg</pre>
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
30 changed files:
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<li class="file-stats">
<a href="#f07866736216be0ee2aba49e392191aeae700a35" style="color: #1068bf;">
build.gradle
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<li class="file-stats">
<a href="#1fa2570ced8b3c33e4b3bd1f563ab3786ec64e29" style="color: #1068bf;">
src/main/java/picard/cmdline/CommandLineProgram.java
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<li class="file-stats">
<a href="#f7d76d352dfb807611c35d4412191ed995aa7003" style="color: #1068bf;">
src/main/java/picard/fingerprint/CrosscheckFingerprints.java
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<li class="file-stats">
<a href="#b8553f759ce8bc72a7ed6f6994097c2fc323b375" style="color: #1068bf;">
src/main/java/picard/fingerprint/FingerprintChecker.java
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<li class="file-stats">
<a href="#6d29efa301dfe7d55a00774547f4cf67aea4ef28" style="color: #1068bf;">
src/main/java/picard/util/SequenceDictionaryUtils.java
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<li class="file-stats">
<a href="#e49bb5587beb891c29297afe9cf94c80c95edd7e" style="color: #1068bf;">
src/test/java/picard/analysis/artifacts/CollectSequencingArtifactMetricsTest.java
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<li class="file-stats">
<a href="#6dac1c7c1b4d9022ddd3bc5f57a44bb077b0983c" style="color: #1068bf;">
src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
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<li class="file-stats">
<a href="#e1d370246779010899b4d52a55c98c9ac1af3784" style="color: #1068bf;">
src/test/java/picard/analysis/replicates/CollectIndependentReplicatesMetricTest.java
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<li class="file-stats">
<a href="#1e6b578642f95f7a451ba037531db2fafb4b5701" style="color: #1068bf;">
src/test/java/picard/fastq/BamToBfqTest.java
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<li class="file-stats">
<a href="#05be7520b4dd89a3de09be1dbab026d6561fd3b1" style="color: #1068bf;">
src/test/java/picard/fingerprint/CrosscheckFingerprintsTest.java
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</li>
<li class="file-stats">
<a href="#8e47b09e231ce09b8b2b713f2020679c7cc00327" style="color: #1068bf;">
src/test/java/picard/fingerprint/FingerprintCheckerTest.java
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<li class="file-stats">
<a href="#41e770699927a5a3306b5a5722b75be3e3ae1299" style="color: #1068bf;">
src/test/java/picard/illumina/CheckIlluminaDirectoryTest.java
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<li class="file-stats">
<a href="#4a3455d3b3da89fba102450e92ca3771afab474e" style="color: #1068bf;">
src/test/java/picard/illumina/CollectIlluminaBasecallingMetricsTest.java
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<li class="file-stats">
<a href="#e1b7610ac081822bc869b241576e7cb24565e95a" style="color: #1068bf;">
src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java
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<li class="file-stats">
<a href="#98e96985ec6ebe536f106ab2bb736999afc79ff9" style="color: #1068bf;">
src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java
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<li class="file-stats">
<a href="#a09216193085cd02d8bb25e1c7a366cf40058c11" style="color: #1068bf;">
src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java
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<li class="file-stats">
<a href="#5266112e051618c9a333e2b3a23bb5ae66a1d756" style="color: #1068bf;">
src/test/java/picard/illumina/parser/BclParserTest.java
</a>
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<li class="file-stats">
<a href="#a795b3663ce9176b8ec9a3b2d6be1522e27f1abe" style="color: #1068bf;">
src/test/java/picard/illumina/parser/IlluminaFileUtilTest.java
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<li class="file-stats">
<a href="#85dfc66eaf47ac9c1c3161200f4a5b3cb5f42375" style="color: #1068bf;">
src/test/java/picard/metrics/CollectRrbsMetricsTest.java
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<li class="file-stats">
<a href="#2fd364663723790d1032a20b6431f11595ce86b7" style="color: #1068bf;">
src/test/java/picard/sam/CramCompatibilityTest.java
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<li class="file-stats">
<a href="#87eb96dd4278db070a5194dd635e14c6a00916bc" style="color: #1068bf;">
src/test/java/picard/sam/DownsampleSamTest.java
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<li class="file-stats">
<a href="#0bccb793326d5b09eb75da1c7a51748a00fbba28" style="color: #1068bf;">
src/test/java/picard/sam/PositionBasedDownsampleSamTest.java
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<li class="file-stats">
<a href="#f5dc81fafe32fa8c26317f0f7de65d3ce459aa32" style="color: #1068bf;">
src/test/java/picard/sam/SamErrorMetric/CollectSamErrorMetricsTest.java
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<li class="file-stats">
<a href="#f815071f7cb02f0ca6502a227eb0fcafcba2a5db" style="color: #1068bf;">
src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java
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<li class="file-stats">
<a href="#9b61479b138e0828830ad8e1bf311e6211bb1976" style="color: #1068bf;">
src/test/java/picard/sam/testers/SamFileTester.java
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</li>
<li class="file-stats">
<a href="#49c1cbf60587a991ee6ceb695512094cb3c765e9" style="color: #1068bf;">
src/test/java/picard/util/IntervalListToolsTest.java
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</li>
<li class="file-stats">
<a href="#e6b8ac7829c30ddf0e78348a6f4b3e9668bd2135" style="color: #1068bf;">
src/test/java/picard/util/LiftoverVcfTest.java
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</li>
<li class="file-stats">
<a href="#520f8f8b364d36f23cb65a0e37149aa8c098d2b8" style="color: #1068bf;">
src/test/java/picard/vcf/GenotypeConcordanceTest.java
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</li>
<li class="file-stats">
<a href="#1e6d1c5c2b8bc592346163b627a4696120cc4084" style="color: #1068bf;">
src/test/java/picard/vcf/SplitVcfsTest.java
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</li>
<li class="file-stats">
<a href="#62dcd1824a15aec744587bfefd9d29b6a6f0b993" style="color: #1068bf;">
src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java
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</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: 0.875rem;">
The diff was not included because it is too large.
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<p style="font-size: small; color: #666;">
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