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 <[email protected]> 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(-) -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
