[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 2.27.5+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / picard-tools


Commits:
ac518bb5 by Pierre Gruet at 2022-11-01T20:28:47+01:00
New upstream version 2.27.5+dfsg
- - - - -


30 changed files:

- build.gradle
- src/main/java/picard/cmdline/CommandLineProgram.java
- src/main/java/picard/fingerprint/CrosscheckFingerprints.java
- src/main/java/picard/fingerprint/FingerprintChecker.java
- src/main/java/picard/util/SequenceDictionaryUtils.java
- src/test/java/picard/analysis/artifacts/CollectSequencingArtifactMetricsTest.java
- src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
- src/test/java/picard/analysis/replicates/CollectIndependentReplicatesMetricTest.java
- src/test/java/picard/fastq/BamToBfqTest.java
- src/test/java/picard/fingerprint/CrosscheckFingerprintsTest.java
- src/test/java/picard/fingerprint/FingerprintCheckerTest.java
- src/test/java/picard/illumina/CheckIlluminaDirectoryTest.java
- src/test/java/picard/illumina/CollectIlluminaBasecallingMetricsTest.java
- src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java
- src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java
- src/test/java/picard/illumina/IlluminaLaneMetricsCollectorTest.java
- src/test/java/picard/illumina/parser/BclParserTest.java
- src/test/java/picard/illumina/parser/IlluminaFileUtilTest.java
- src/test/java/picard/metrics/CollectRrbsMetricsTest.java
- src/test/java/picard/sam/CramCompatibilityTest.java
- src/test/java/picard/sam/DownsampleSamTest.java
- src/test/java/picard/sam/PositionBasedDownsampleSamTest.java
- src/test/java/picard/sam/SamErrorMetric/CollectSamErrorMetricsTest.java
- src/test/java/picard/sam/markduplicates/MarkDuplicatesTest.java
- src/test/java/picard/sam/testers/SamFileTester.java
- src/test/java/picard/util/IntervalListToolsTest.java
- src/test/java/picard/util/LiftoverVcfTest.java
- src/test/java/picard/vcf/GenotypeConcordanceTest.java
- src/test/java/picard/vcf/SplitVcfsTest.java
- src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/ac518bb5f410586638e4af3f2a8c885ac740b525

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/ac518bb5f410586638e4af3f2a8c885ac740b525
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