[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 2.24.0+dfsg

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch upstream at Debian Med / picard-tools


Commits:
a51591b3 by Michael R. Crusoe at 2021-01-07T13:41:43+01:00
New upstream version 2.24.0+dfsg
- - - - -


30 changed files:

- src/main/java/picard/analysis/AlignmentSummaryMetrics.java
- src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
- src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
- src/main/java/picard/analysis/CollectBaseDistributionByCycle.java
- src/main/java/picard/analysis/CollectGcBiasMetrics.java
- src/main/java/picard/analysis/CollectInsertSizeMetrics.java
- src/main/java/picard/analysis/CollectMultipleMetrics.java
- src/main/java/picard/analysis/CollectRnaSeqMetrics.java
- src/main/java/picard/analysis/CollectRrbsMetrics.java
- src/main/java/picard/analysis/CollectWgsMetrics.java
- src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java
- src/main/java/picard/analysis/MeanQualityByCycle.java
- src/main/java/picard/analysis/QualityScoreDistribution.java
- src/main/java/picard/analysis/directed/PanelMetricsBase.java
- src/main/java/picard/analysis/directed/TargetMetricsCollector.java
- src/main/java/picard/analysis/replicates/CollectIndependentReplicateMetrics.java
- src/main/java/picard/arrays/GtcToVcf.java
- src/main/java/picard/cmdline/CommandLineProgram.java
- − src/main/java/picard/illumina/parser/ClusterIntensityFileReader.java
- − src/main/java/picard/illumina/parser/FourChannelIntensityData.java
- src/main/java/picard/illumina/parser/IlluminaData.java
- src/main/java/picard/illumina/parser/ReadData.java
- src/main/java/picard/sam/BuildBamIndex.java
- src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java
- src/main/java/picard/sam/SamErrorMetric/ReadBaseStratification.java
- src/main/java/picard/sam/ValidateSamFile.java
- src/main/java/picard/sam/util/PhysicalLocation.java
- src/main/java/picard/sam/util/ReadNameParser.java
- src/main/java/picard/util/IntervalListTools.java
- src/main/java/picard/vcf/MendelianViolations/FindMendelianViolations.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/a51591b391fe3a248a9e1ddc74a654c204764350

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/a51591b391fe3a248a9e1ddc74a654c204764350
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