[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 2.27.4+dfsg

[Pierre Gruet (@pgt)]

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


Commits:
f17ae3a5 by Pierre Gruet at 2022-09-22T16:29:27+02:00
New upstream version 2.27.4+dfsg
- - - - -


30 changed files:

- .gitignore
- build.gradle
- src/main/java/picard/analysis/AlignmentSummaryMetrics.java
- src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java
- src/main/java/picard/analysis/CollectQualityYieldMetrics.java
- + src/main/java/picard/analysis/HistogramGenerator.java
- src/main/java/picard/analysis/MeanQualityByCycle.java
- src/main/java/picard/sam/DuplicationMetrics.java
- + src/main/java/picard/sam/DuplicationMetricsFactory.java
- src/main/java/picard/sam/FastqToSam.java
- + src/main/java/picard/sam/FlowBasedDuplicationMetrics.java
- src/main/java/picard/sam/RevertSam.java
- src/main/java/picard/sam/markduplicates/CollectDuplicateMetrics.java
- src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java
- src/main/java/picard/sam/markduplicates/MarkDuplicates.java
- + src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowArgumentCollection.java
- + src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowHelper.java
- + src/main/java/picard/sam/markduplicates/MarkDuplicatesHelper.java
- src/main/java/picard/sam/markduplicates/MarkDuplicatesWithMateCigarIterator.java
- src/main/java/picard/sam/markduplicates/SimpleMarkDuplicatesWithMateCigar.java
- src/main/java/picard/sam/markduplicates/util/AbstractMarkDuplicatesCommandLineProgram.java
- src/main/java/picard/sam/markduplicates/util/LibraryIdGenerator.java
- src/main/java/picard/sam/markduplicates/util/ReadEnds.java
- src/main/java/picard/sam/markduplicates/util/ReadEndsForMarkDuplicates.java
- src/main/java/picard/util/AccumulateQualityYieldMetrics.java
- src/main/java/picard/vcf/GenotypeConcordance.java
- src/test/java/picard/analysis/CollectQualityYieldMetricsTest.java
- src/test/java/picard/sam/CramCompatibilityTest.java
- src/test/java/picard/sam/DuplicationMetricsTest.java
- src/test/java/picard/sam/FastqToSamTest.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/f17ae3a5adf9516c80a4e5d57455fa80fe172c0f

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/commit/f17ae3a5adf9516c80a4e5d57455fa80fe172c0f
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