[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 2.18.25+dfsg

[Olivier Sallou]

Olivier Sallou pushed to branch upstream at Debian Med / picard-tools


Commits:
ebc5863a by Olivier Sallou at 2019-01-25T10:43:57Z
New upstream version 2.18.25+dfsg
- - - - -


30 changed files:

- Dockerfile
- build.gradle
- + src/main/java/picard/sam/AddOATag.java
- src/main/java/picard/sam/markduplicates/MarkDuplicates.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/OpticalDuplicateFinder.java
- src/main/java/picard/sam/util/PGTagArgumentCollection.java
- src/main/java/picard/util/LiftoverUtils.java
- src/main/java/picard/vcf/LiftoverVcf.java
- + src/test/java/picard/sam/AddOATagTest.java
- src/test/java/picard/sam/CompareSAMsTest.java
- src/test/java/picard/sam/ValidateSamFileTest.java
- src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTester.java
- + src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTest.java
- + src/test/java/picard/sam/markduplicates/MarkDuplicatesSetSizeHistogramTester.java
- src/test/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigarTester.java
- src/test/java/picard/sam/markduplicates/util/OpticalDuplicateFinderTest.java
- src/test/java/picard/sam/testers/SamFileTester.java
- src/test/java/picard/util/LiftoverVcfTest.java
- src/test/java/picard/vcf/VcfTestUtils.java
- testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list
- testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam
- testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam
- testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam
- testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam
- testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list
- testdata/picard/fingerprint/reference.dict
- testdata/picard/illumina/151T8B8B151T_cbcl/sams/1102.CACCTAGTACTCGAGT.sam
- testdata/picard/illumina/151T8B8B151T_cbcl/sams/1102.CCCCGCTTTTGCGTGT.sam


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/commit/ebc5863a824a4ddb1e24754f070e6d109a2c22e5

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/commit/ebc5863a824a4ddb1e24754f070e6d109a2c22e5
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