[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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