[med-svn] [Git][med-team/picard-tools][master] 7 commits: New upstream version 2.18.17+dfsg

[Andreas Tille]

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


Commits:
4b641b5f by Andreas Tille at 2018-12-01T07:02:24Z
New upstream version 2.18.17+dfsg
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3e087d26 by Andreas Tille at 2018-12-01T07:03:16Z
Update upstream source from tag 'upstream/2.18.17+dfsg'

Update to upstream version '2.18.17+dfsg'
with Debian dir 0630852ae1c97db245361e03a44bbc06602226f3
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649b6cb1 by Andreas Tille at 2018-12-01T07:03:17Z
New upstream version

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08ce271c by Andreas Tille at 2018-12-01T07:04:10Z
Secure URI in copyright format

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9b4f6338 by Andreas Tille at 2018-12-01T07:04:10Z
Remove trailing whitespace in debian/changelog

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a6af6456 by Andreas Tille at 2018-12-01T07:04:10Z
Remove trailing whitespace in debian/control

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84f8db61 by Andreas Tille at 2018-12-01T07:04:10Z
Remove trailing whitespace in debian/rules

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30 changed files:

- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- 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


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/9359e09f6df2c08b2f2ec3269c9243b8ef06c449...84f8db6109024cf2baebd99e997bbd3e746003b9

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View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/9359e09f6df2c08b2f2ec3269c9243b8ef06c449...84f8db6109024cf2baebd99e997bbd3e746003b9
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