[med-svn] [picard-tools] branch master updated (bc66a49 -> 1489b2e)

Andreas Tille tille at debian.org
Sat Sep 10 08:51:29 UTC 2016


This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository picard-tools.

      from  bc66a49   Cleanup build dependencies
       new  2968317   New upstream version 2.6.0+dfsg
       new  a3708a3   Merge changelogs
       new  8385d41   Merge changes
       new  4c51b3d   Adapt patches
       new  fa00cd4   d/copyright: remove *.bak files which are removed in clean target anyway
       new  1489b2e   New upstream version 2.6.0+dfsg

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .travis.yml                                        |   2 +
 README.md                                          |  74 ++++++-
 build.gradle                                       |  25 ++-
 build.xml                                          |   3 +
 debian/changelog                                   |  10 +-
 debian/control                                     |   4 +-
 debian/copyright                                   |   1 +
 debian/patches/10-build.xml.patch                  |  25 +--
 settings.gradle                                    |   1 +
 .../analysis/directed/RnaSeqMetricsCollector.java  |  45 +++--
 .../picard/fingerprint/FingerprintChecker.java     |   4 +-
 .../java/picard/fingerprint/GenotypeReader.java    |   2 +-
 src/main/java/picard/sam/BuildBamIndex.java        |   4 +-
 src/main/java/picard/sam/FastqToSam.java           |   4 +-
 src/main/java/picard/sam/FilterSamReads.java       |  60 ++++--
 src/main/java/picard/vcf/FixVcfHeader.java         | 214 +++++++++++++++++++++
 src/main/java/picard/vcf/GatherVcfs.java           |   2 +-
 src/main/java/picard/vcf/MakeSitesOnlyVcf.java     |   2 +-
 src/main/java/picard/vcf/MergeVcfs.java            |   2 +-
 src/main/java/picard/vcf/SortVcf.java              |   4 +-
 src/main/java/picard/vcf/SplitVcfs.java            |   2 +-
 .../picard/vcf/UpdateVcfSequenceDictionary.java    |   2 +-
 src/main/java/picard/vcf/VcfFormatConverter.java   |   2 +-
 .../vcf/processor/VariantIteratorProducer.java     |   6 +-
 src/test/java/picard/sam/FilterSamReadsTest.java   | 104 ++++++++--
 .../picard/vcf/AbstractVcfMergingClpTester.java    |   2 +-
 src/test/java/picard/vcf/FixVcfHeaderTest.java     |  94 +++++++++
 .../picard/vcf/VariantContextComparatorTest.java   |   2 +-
 .../sams_with_4M/indicies/AAAAAAAA.sam.bak         |   2 -
 .../sams_with_4M/indicies/AAAAGAAG.sam.bak         |   2 -
 .../sams_with_4M/indicies/AACAATGG.sam.bak         |   6 -
 .../sams_with_4M/indicies/AACGCATT.sam.bak         |   9 -
 .../sams_with_4M/indicies/ACAAAATT.sam.bak         |   2 -
 .../sams_with_4M/indicies/ACAGGTAT.sam.bak         |   6 -
 .../sams_with_4M/indicies/ACAGTTGA.sam.bak         |   4 -
 .../sams_with_4M/indicies/ACCAGTTG.sam.bak         |   2 -
 .../sams_with_4M/indicies/ACGAAATC.sam.bak         |   2 -
 .../sams_with_4M/indicies/ACTAAGAC.sam.bak         |   6 -
 .../sams_with_4M/indicies/ACTGTACC.sam.bak         |   2 -
 .../sams_with_4M/indicies/ACTGTATC.sam.bak         |   6 -
 .../sams_with_4M/indicies/AGAAAAGA.sam.bak         |   2 -
 .../sams_with_4M/indicies/AGCATGGA.sam.bak         |   5 -
 .../sams_with_4M/indicies/AGGTAAGG.sam.bak         |   6 -
 .../sams_with_4M/indicies/AGGTCGCA.sam.bak         |   6 -
 .../sams_with_4M/indicies/ATTATCAA.sam.bak         |   7 -
 .../sams_with_4M/indicies/ATTCCTCT.sam.bak         |   6 -
 .../sams_with_4M/indicies/CAACTCTC.sam.bak         |   7 -
 .../sams_with_4M/indicies/CAATAGAC.sam.bak         |   2 -
 .../sams_with_4M/indicies/CAATAGTC.sam.bak         |   9 -
 .../sams_with_4M/indicies/CAGCGGAT.sam.bak         |   2 -
 .../sams_with_4M/indicies/CAGCGGTA.sam.bak         |   7 -
 .../sams_with_4M/indicies/CCAACATT.sam.bak         |   9 -
 .../sams_with_4M/indicies/CCAGCACC.sam.bak         |   5 -
 .../sams_with_4M/indicies/CCATGCGT.sam.bak         |   2 -
 .../sams_with_4M/indicies/CGCCTTCC.sam.bak         |   4 -
 .../sams_with_4M/indicies/CGCTATGT.sam.bak         |   7 -
 .../sams_with_4M/indicies/CTAACTCG.sam.bak         |   6 -
 .../sams_with_4M/indicies/CTATGCGC.sam.bak         |   2 -
 .../sams_with_4M/indicies/CTATGCGT.sam.bak         |   9 -
 .../sams_with_4M/indicies/CTGCGGAT.sam.bak         |   5 -
 .../sams_with_4M/indicies/CTGTAATC.sam.bak         |   8 -
 .../sams_with_4M/indicies/GAAAAAAA.sam.bak         |   2 -
 .../sams_with_4M/indicies/GAACGAT..sam.bak         |   2 -
 .../sams_with_4M/indicies/GAAGGAAG.sam.bak         |   5 -
 .../sams_with_4M/indicies/GACCAGGA.sam.bak         |   9 -
 .../sams_with_4M/indicies/GACCAGGC.sam.bak         |   2 -
 .../sams_with_4M/indicies/GACCGTTG.sam.bak         |   6 -
 .../sams_with_4M/indicies/GACCTAAC.sam.bak         |   3 -
 .../sams_with_4M/indicies/GATATCCA.sam.bak         |   5 -
 .../sams_with_4M/indicies/GCCGTCGA.sam.bak         |   7 -
 .../sams_with_4M/indicies/GCCTAGCC.sam.bak         |   7 -
 .../sams_with_4M/indicies/GTAACATC.sam.bak         |   4 -
 .../sams_with_4M/indicies/GTCCACAG.sam.bak         |   4 -
 .../25T8B25T/sams_with_4M/indicies/N.sam.bak       |  18 --
 .../sams_with_4M/indicies/TAAGCACA.sam.bak         |   4 -
 .../sams_with_4M/indicies/TACCGTCT.sam.bak         |   2 -
 .../sams_with_4M/indicies/TAGCGGTA.sam.bak         |   2 -
 .../sams_with_4M/indicies/TATCAGCC.sam.bak         |   2 -
 .../sams_with_4M/indicies/TATCCAGG.sam.bak         |   6 -
 .../sams_with_4M/indicies/TATCCATG.sam.bak         |   2 -
 .../sams_with_4M/indicies/TATCTCGG.sam.bak         |   2 -
 .../sams_with_4M/indicies/TATCTGCC.sam.bak         |   9 -
 .../sams_with_4M/indicies/TCCGTCTA.sam.bak         |   2 -
 .../sams_with_4M/indicies/TCGCTAGA.sam.bak         |   7 -
 .../sams_with_4M/indicies/TCTGCAAG.sam.bak         |   3 -
 .../sams_with_4M/indicies/TGCAAGTA.sam.bak         |   4 -
 .../sams_with_4M/indicies/TGCTGCTG.sam.bak         |   6 -
 .../sams_with_4M/indicies/TGTAACTC.sam.bak         |   3 -
 .../sams_with_4M/indicies/TGTAATCA.sam.bak         |   5 -
 .../sams_with_4M/indicies/TTGTCTAT.sam.bak         |   6 -
 .../sam/FilterSamReads/filter1.interval_list       |  12 ++
 .../sam/FilterSamReads/filter2.interval_list       |  12 ++
 testdata/picard/vcf/FixVcfHeaderTest/header.vcf    | 150 +++++++++++++++
 .../FixVcfHeaderTest/header_with_extra_sample.vcf  | 150 +++++++++++++++
 testdata/picard/vcf/FixVcfHeaderTest/input.vcf     | 199 +++++++++++++++++++
 testdata/picard/vcf/FixVcfHeaderTest/output.vcf    | 206 ++++++++++++++++++++
 96 files changed, 1327 insertions(+), 408 deletions(-)
 create mode 100644 settings.gradle
 create mode 100644 src/main/java/picard/vcf/FixVcfHeader.java
 create mode 100644 src/test/java/picard/vcf/FixVcfHeaderTest.java
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAAAAA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAGAAG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACAATGG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACGCATT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAAAATT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGGTAT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGTTGA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACCAGTTG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACGAAATC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTAAGAC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTACC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTATC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGAAAAGA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGCATGGA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTAAGG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTCGCA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTATCAA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTCCTCT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAACTCTC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGAC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGTC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGAT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGTA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAACATT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAGCACC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCATGCGT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCCTTCC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCTATGT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTAACTCG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGCGGAT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGTAATC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAAAAAA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAACGAT..sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAGGAAG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCGTTG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCTAAC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GATATCCA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCGTCGA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCTAGCC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTAACATC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTCCACAG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/N.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAAGCACA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TACCGTCT.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAGCGGTA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCAGCC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCAGG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCATG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTCGG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTGCC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCCGTCTA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCGCTAGA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCTGCAAG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCAAGTA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCTGCTG.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAACTC.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAATCA.sam.bak
 delete mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TTGTCTAT.sam.bak
 create mode 100644 testdata/picard/sam/FilterSamReads/filter1.interval_list
 create mode 100644 testdata/picard/sam/FilterSamReads/filter2.interval_list
 create mode 100644 testdata/picard/vcf/FixVcfHeaderTest/header.vcf
 create mode 100644 testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf
 create mode 100644 testdata/picard/vcf/FixVcfHeaderTest/input.vcf
 create mode 100644 testdata/picard/vcf/FixVcfHeaderTest/output.vcf

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