[med-svn] [picard-tools] branch upstream updated (9175c40 -> 0ce17ad)
Andreas Tille
tille at debian.org
Sat Sep 10 08:46:23 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository picard-tools.
from 9175c40 Imported Upstream version 2.5.0-gradle+dfsg
new 1d84a5c New upstream version 2.6.0+dfsg
new 0ce17ad New upstream version 2.6.0+dfsg
The 2 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 +
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 ++++++++++++++++++++
92 files changed, 1307 insertions(+), 388 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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