[med-svn] [picard-tools] 01/07: Merge tag 'upstream/1.105'
Olivier Sallou
osallou at debian.org
Tue Dec 24 10:42:49 UTC 2013
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository picard-tools.
commit 3d60f1033e02fb0a228d61a38234bb9345c7fe84
Merge: fa4a3a6 711211f
Author: Olivier Sallou <olivier.sallou at debian.org>
Date: Tue Dec 24 11:14:59 2013 +0100
Merge tag 'upstream/1.105'
Upstream version 1.105
Picard-public.ipr | 4 +
build.xml | 6 +-
src/c/inteldeflater/IntelDeflater.c | 247 +++++++++
.../net/sf/picard/cmdline/CommandLineProgram.java | 6 +-
src/java/net/sf/picard/fastq/BasicFastqWriter.java | 19 +-
.../sf/picard/fastq/Casava18ReadNameEncoder.java | 46 ++
src/java/net/sf/picard/fastq/FastqReader.java | 33 +-
.../net/sf/picard/fastq/FastqWriterFactory.java | 6 +-
.../sf/picard/fastq/IlluminaReadNameEncoder.java | 28 +
src/java/net/sf/picard/fastq/ReadNameEncoder.java | 17 +
.../picard/illumina/ClusterDataToSamConverter.java | 10 +-
.../picard/illumina/ExtractIlluminaBarcodes.java | 246 +++++----
.../picard/illumina/IlluminaBasecallsToFastq.java | 86 +++-
.../parser/readers/TileMetricsOutReader.java | 9 +-
src/java/net/sf/picard/io/IoUtil.java | 12 +-
.../net/sf/picard/metrics/MultiLevelCollector.java | 36 +-
src/java/net/sf/picard/pedigree/PedFile.java | 99 ++++
src/java/net/sf/picard/pedigree/PedTrio.java | 45 ++
src/java/net/sf/picard/pedigree/Sex.java | 26 +
src/java/net/sf/picard/sam/FastqToSam.java | 14 +-
src/java/net/sf/picard/sam/SamToFastq.java | 9 +-
src/java/net/sf/picard/sam/ValidateSamFile.java | 5 +-
src/java/net/sf/picard/util/IlluminaUtil.java | 9 -
src/java/net/sf/picard/util/IntervalUtil.java | 21 +-
src/java/net/sf/picard/util/MathUtil.java | 125 ++++-
src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 2 +-
src/java/net/sf/samtools/Defaults.java | 9 +
.../net/sf/samtools/SAMSequenceDictionary.java | 28 +
src/java/net/sf/samtools/SAMSequenceRecord.java | 10 +
src/java/net/sf/samtools/SAMUtils.java | 2 +-
.../seekablestream/ISeekableStreamFactory.java | 33 ++
.../samtools/seekablestream/SeekableFTPStream.java | 2 +-
.../seekablestream/SeekableStreamFactory.java | 56 +-
.../samtools/util/BlockCompressedOutputStream.java | 8 +-
src/java/net/sf/samtools/util/CollectionUtil.java | 8 +
src/java/net/sf/samtools/util/IOUtil.java | 2 +-
src/java/net/sf/samtools/util/Iso8601Date.java | 2 +-
src/java/net/sf/samtools/util/Lazy.java | 35 ++
.../net/sf/samtools/util/RelativeIso8601Date.java | 187 +++++++
src/java/net/sf/samtools/util/StringUtil.java | 5 +
src/java/net/sf/samtools/util/ftp/FTPUtils.java | 20 +-
.../net/sf/samtools/util/zip/DeflaterFactory.java | 78 +++
.../net/sf/samtools/util/zip/IntelDeflater.java | 567 +++++++++++++++++++++
src/java/net/sf/samtools/util/zip/ZStreamRef.java | 48 ++
.../org/broad/tribble/AbstractFeatureReader.java | 47 +-
src/java/org/broad/tribble/TabixFeatureReader.java | 5 +
src/java/org/broad/tribble/Tribble.java | 5 +-
.../broad/tribble/TribbleIndexedFeatureReader.java | 10 +-
.../org/broad/tribble/readers/TabixReader.java | 23 +-
src/java/org/broad/tribble/util/ParsingUtils.java | 29 ++
.../variant/variantcontext/VariantContext.java | 47 ++
.../variantcontext/VariantContextComparator.java | 23 +-
.../variantcontext/VariantContextUtils.java | 61 ++-
.../variant/variantcontext/writer/BCF2Writer.java | 27 +-
.../writer/IndexingVariantContextWriter.java | 82 ++-
.../writer/IntGenotypeFieldAccessors.java | 2 +-
.../variant/variantcontext/writer/VCFWriter.java | 499 +++---------------
.../writer/VariantContextWriterFactory.java | 21 +-
.../variant/vcf/AbstractVCFCodec.java | 26 +-
.../org/broadinstitute/variant/vcf/VCFCodec.java | 4 +-
.../variant/vcf/VCFContigHeaderLine.java | 2 +-
.../org/broadinstitute/variant/vcf/VCFEncoder.java | 381 ++++++++++++++
.../broadinstitute/variant/vcf/VCFFileReader.java | 40 +-
.../org/broadinstitute/variant/vcf/VCFHeader.java | 4 +-
.../broadinstitute/variant/vcf/VCFRecordCodec.java | 63 +++
src/scripts/build_intel_deflater.sh | 64 +++
.../net/sf/picard/analysis/rnaSeqCoverage.R | 43 +-
src/scripts/release_picard.sh | 3 +-
.../illumina/IlluminaBasecallsToFastqTest.java | 16 +-
src/tests/java/net/sf/picard/io/IoUtilTest.java | 12 +
.../java/net/sf/picard/sam/FastqToSamTest.java | 77 +--
.../java/net/sf/picard/sam/SamToFastqTest.java | 3 +-
.../java/net/sf/picard/util/MathUtilTest.java | 45 ++
.../java/net/sf/picard/vcf/SplitVcfsTest.java | 16 +-
.../sf/samtools/util/RelativeIso8601DateTest.java | 39 ++
.../variantcontext/VariantJEXLContextUnitTest.java | 2 +-
.../variantcontext/writer/VCFWriterUnitTest.java | 54 +-
.../broadinstitute/variant/vcf/VCFEncoderTest.java | 45 ++
.../IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq | 26 +-
.../AACTTGAC.barcode_1.fastq | 26 +-
.../AACTTGACTTGAGCCT.1.fastq | 26 +-
.../AACTTGACTTGAGCCT.barcode_1.fastq | 26 +-
.../AACTTGACTTGAGCCT.barcode_2.fastq | 26 +-
.../IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq | 26 +-
.../AAGGATGT.barcode_1.fastq | 26 +-
.../AAGGATGTTTCGCTGA.1.fastq | 26 +-
.../AAGGATGTTTCGCTGA.barcode_1.fastq | 26 +-
.../AAGGATGTTTCGCTGA.barcode_2.fastq | 26 +-
.../IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq | 18 +-
.../ACCAACTG.barcode_1.fastq | 18 +-
.../ACCAACTGTGTCGGAT.1.fastq | 18 +-
.../ACCAACTGTGTCGGAT.barcode_1.fastq | 18 +-
.../ACCAACTGTGTCGGAT.barcode_2.fastq | 18 +-
.../IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq | 16 +-
.../AGCAATTC.barcode_1.fastq | 16 +-
.../AGCAATTCTGCTCGAC.1.fastq | 16 +-
.../AGCAATTCTGCTCGAC.barcode_1.fastq | 16 +-
.../AGCAATTCTGCTCGAC.barcode_2.fastq | 16 +-
.../IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq | 16 +-
.../AGTTGCTT.barcode_1.fastq | 16 +-
.../AGTTGCTTTCTGGCGA.1.fastq | 16 +-
.../AGTTGCTTTCTGGCGA.barcode_1.fastq | 16 +-
.../AGTTGCTTTCTGGCGA.barcode_2.fastq | 16 +-
.../IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq | 6 +-
.../ATTATGTT.barcode_1.fastq | 6 +-
.../ATTATGTTTCGGAATG.1.fastq | 6 +-
.../ATTATGTTTCGGAATG.barcode_1.fastq | 6 +-
.../ATTATGTTTCGGAATG.barcode_2.fastq | 6 +-
.../IlluminaBasecallsToFastqTest/CACATCCT.1.fastq | 18 +-
.../CACATCCT.barcode_1.fastq | 18 +-
.../CACATCCTTACTTAGC.1.fastq | 18 +-
.../CACATCCTTACTTAGC.barcode_1.fastq | 18 +-
.../CACATCCTTACTTAGC.barcode_2.fastq | 18 +-
.../IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq | 18 +-
.../CAGGAGCC.barcode_1.fastq | 18 +-
.../CAGGAGCCGTATAACA.1.fastq | 18 +-
.../CAGGAGCCGTATAACA.barcode_1.fastq | 18 +-
.../CAGGAGCCGTATAACA.barcode_2.fastq | 18 +-
.../IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq | 24 +-
.../CATAGCGA.barcode_1.fastq | 24 +-
.../CATAGCGAGGTCCAGA.1.fastq | 24 +-
.../CATAGCGAGGTCCAGA.barcode_1.fastq | 24 +-
.../CATAGCGAGGTCCAGA.barcode_2.fastq | 24 +-
.../IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq | 10 +-
.../CATGCTTA.barcode_1.fastq | 10 +-
.../CATGCTTAGCACATCT.1.fastq | 10 +-
.../CATGCTTAGCACATCT.barcode_1.fastq | 10 +-
.../CATGCTTAGCACATCT.barcode_2.fastq | 10 +-
.../IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq | 22 +-
.../CCAGTTAG.barcode_1.fastq | 22 +-
.../CCAGTTAGGCACACGA.1.fastq | 22 +-
.../CCAGTTAGGCACACGA.barcode_1.fastq | 22 +-
.../CCAGTTAGGCACACGA.barcode_2.fastq | 22 +-
.../IlluminaBasecallsToFastqTest/CCTACCAT.1.fastq | 4 +-
.../CCTACCAT.barcode_1.fastq | 4 +-
.../CCTACCATCTACCAGG.1.fastq | 4 +-
.../CCTACCATCTACCAGG.barcode_1.fastq | 4 +-
.../CCTACCATCTACCAGG.barcode_2.fastq | 4 +-
.../IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq | 12 +-
.../CTACCAGG.barcode_1.fastq | 12 +-
.../CTACCAGGCCTACCAT.1.fastq | 12 +-
.../CTACCAGGCCTACCAT.barcode_1.fastq | 12 +-
.../CTACCAGGCCTACCAT.barcode_2.fastq | 12 +-
.../IlluminaBasecallsToFastqTest/GCACACGA.1.fastq | 18 +-
.../GCACACGA.barcode_1.fastq | 18 +-
.../GCACACGACCAGTTAG.1.fastq | 18 +-
.../GCACACGACCAGTTAG.barcode_1.fastq | 18 +-
.../GCACACGACCAGTTAG.barcode_2.fastq | 18 +-
.../IlluminaBasecallsToFastqTest/GCACATCT.1.fastq | 6 +-
.../GCACATCT.barcode_1.fastq | 6 +-
.../GCACATCTCATGCTTA.1.fastq | 6 +-
.../GCACATCTCATGCTTA.barcode_1.fastq | 6 +-
.../GCACATCTCATGCTTA.barcode_2.fastq | 6 +-
.../IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq | 14 +-
.../GGTCCAGA.barcode_1.fastq | 14 +-
.../GGTCCAGACATAGCGA.1.fastq | 14 +-
.../GGTCCAGACATAGCGA.barcode_1.fastq | 14 +-
.../GGTCCAGACATAGCGA.barcode_2.fastq | 14 +-
.../IlluminaBasecallsToFastqTest/GTATAACA.1.fastq | 20 +-
.../GTATAACA.barcode_1.fastq | 20 +-
.../GTATAACACAGGAGCC.1.fastq | 20 +-
.../GTATAACACAGGAGCC.barcode_1.fastq | 20 +-
.../GTATAACACAGGAGCC.barcode_2.fastq | 20 +-
.../IlluminaBasecallsToFastqTest/N.1.fastq | 446 ++++++++--------
.../IlluminaBasecallsToFastqTest/N.barcode_1.fastq | 446 ++++++++--------
.../IlluminaBasecallsToFastqTest/NN.1.fastq | 446 ++++++++--------
.../NN.barcode_1.fastq | 446 ++++++++--------
.../NN.barcode_2.fastq | 446 ++++++++--------
.../IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq | 16 +-
.../TACTTAGC.barcode_1.fastq | 16 +-
.../TACTTAGCCACATCCT.1.fastq | 16 +-
.../TACTTAGCCACATCCT.barcode_1.fastq | 16 +-
.../TACTTAGCCACATCCT.barcode_2.fastq | 16 +-
.../IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq | 14 +-
.../TCGGAATG.barcode_1.fastq | 14 +-
.../TCGGAATGATTATGTT.1.fastq | 14 +-
.../TCGGAATGATTATGTT.barcode_1.fastq | 14 +-
.../TCGGAATGATTATGTT.barcode_2.fastq | 14 +-
.../IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq | 10 +-
.../TCTGGCGA.barcode_1.fastq | 10 +-
.../TCTGGCGAAGTTGCTT.1.fastq | 10 +-
.../TCTGGCGAAGTTGCTT.barcode_1.fastq | 10 +-
.../TCTGGCGAAGTTGCTT.barcode_2.fastq | 10 +-
.../IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq | 10 +-
.../TGCTCGAC.barcode_1.fastq | 10 +-
.../TGCTCGACAGCAATTC.1.fastq | 10 +-
.../TGCTCGACAGCAATTC.barcode_1.fastq | 10 +-
.../TGCTCGACAGCAATTC.barcode_2.fastq | 10 +-
.../IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq | 8 +-
.../TGTCGGAT.barcode_1.fastq | 8 +-
.../TGTCGGATACCAACTG.1.fastq | 8 +-
.../TGTCGGATACCAACTG.barcode_1.fastq | 8 +-
.../TGTCGGATACCAACTG.barcode_2.fastq | 8 +-
.../IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq | 10 +-
.../TTCGCTGA.barcode_1.fastq | 10 +-
.../TTCGCTGAAAGGATGT.1.fastq | 10 +-
.../TTCGCTGAAAGGATGT.barcode_1.fastq | 10 +-
.../TTCGCTGAAAGGATGT.barcode_2.fastq | 10 +-
.../IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq | 12 +-
.../TTGAGCCT.barcode_1.fastq | 12 +-
.../TTGAGCCTAACTTGAC.1.fastq | 12 +-
.../TTGAGCCTAACTTGAC.barcode_1.fastq | 12 +-
.../TTGAGCCTAACTTGAC.barcode_2.fastq | 12 +-
.../nonBarcoded.1.fastq | 120 ++---
.../nonBarcoded.2.fastq | 120 ++---
testdata/net/sf/picard/io/5newline5.txt | 2 +
testdata/net/sf/picard/io/empty.txt | 0
.../illumina-sanger_full_range_as_sanger-62.fastq | 4 +
.../sf/picard/sam/fastq2bam/ok-paired/pair1.txt | 2 +-
.../sam/fastq2bam/ok-paired/s_1_1_sequence.txt | 40 ++
.../sam/fastq2bam/ok-paired/s_1_2_sequence.txt | 41 ++
.../sam/fastq2bam/ok-paired/s_1_sequence.txt | 40 ++
.../{ok-paired => permissive-format}/pair1.txt | 5 +
.../sam/fastq2bam/permissive-format/pair2.txt | 28 +
.../fastq2bam/permissive-format/s_1_1_sequence.txt | 51 ++
.../fastq2bam/permissive-format/s_1_2_sequence.txt | 41 ++
.../fastq2bam/permissive-format/s_1_sequence.txt | 62 +++
217 files changed, 5659 insertions(+), 2983 deletions(-)
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