[med-svn] [Git][med-team/picard-tools][upstream] New upstream version 2.18.17+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / picard-tools


Commits:
4b641b5f by Andreas Tille at 2018-12-01T07:02:24Z
New upstream version 2.18.17+dfsg
- - - - -


30 changed files:

- src/main/java/picard/analysis/TheoreticalSensitivity.java
- src/main/java/picard/fingerprint/CheckFingerprint.java
- src/main/java/picard/illumina/IlluminaBasecallsToFastq.java
- src/main/java/picard/illumina/IlluminaBasecallsToSam.java
- src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java
- src/main/java/picard/illumina/parser/BaseIlluminaDataProvider.java
- src/main/java/picard/illumina/parser/CbclData.java
- src/main/java/picard/illumina/parser/FilterParser.java
- src/main/java/picard/illumina/parser/IlluminaData.java
- src/main/java/picard/illumina/parser/MultiTileFilterParser.java
- src/main/java/picard/illumina/parser/readers/CbclReader.java
- src/main/java/picard/sam/RevertSam.java
- src/main/java/picard/sam/markduplicates/MarkDuplicates.java
- src/main/java/picard/sam/markduplicates/UmiAwareDuplicateSetIterator.java
- src/main/java/picard/sam/markduplicates/UmiAwareMarkDuplicatesWithMateCigar.java
- src/main/java/picard/sam/markduplicates/UmiGraph.java
- src/main/java/picard/sam/markduplicates/UmiUtil.java
- src/main/java/picard/sam/markduplicates/util/OpticalDuplicateFinder.java
- src/main/java/picard/sam/util/ReadNameParser.java
- src/main/java/picard/util/GraphUtils.java
- + src/main/java/picard/util/IntervalList/IntervalListScatterMode.java
- + src/main/java/picard/util/IntervalList/IntervalListScatterer.java
- + src/main/java/picard/util/IntervalList/IntervalListScattererByBaseCount.java
- + src/main/java/picard/util/IntervalList/IntervalListScattererByIntervalCount.java
- + src/main/java/picard/util/IntervalList/IntervalListScattererWithSubdivision.java
- + src/main/java/picard/util/IntervalList/IntervalListScattererWithoutSubdivision.java
- + src/main/java/picard/util/IntervalList/IntervalListScattererWithoutSubdivisionWithOverflow.java
- − src/main/java/picard/util/IntervalListScatterer.java
- src/main/java/picard/util/IntervalListTools.java
- src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/commit/4b641b5f58cc06f5ca4737981cbfd64c7d2a7899

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/commit/4b641b5f58cc06f5ca4737981cbfd64c7d2a7899
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20181201/7aab4cb8/attachment-0001.html>