[med-svn] [picard-tools] branch master updated (c8be686 -> f458746)
Olivier Sallou
osallou at debian.org
Tue Dec 24 10:42:48 UTC 2013
This is an automated email from the git hooks/post-receive script.
osallou pushed a change to branch master
in repository picard-tools.
from c8be686 Conforms with Policy 3.9.5.
adds 711211f Imported Upstream version 1.105
new 3d60f10 Merge tag 'upstream/1.105'
new 58a41da new upstream release 1.105
new ad07325 adapt patch to latest release
new 71a6fbd but back patch erased by error
new 50fbf31 apply patch on new CBZip2 calls, constructor is different, I selected the False for the headerless parameter in InputStream constructor
new 4ea677d set standards to 3.9.5
new f458746 fix merge with Charles inputs
The 7 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:
Picard-public.ipr | 4 +
build.xml | 6 +-
debian/changelog | 6 +-
debian/copyright | 1 +
debian/patches/use_libjbzip2-java | 10 +-
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/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 | 110 +++-
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/Lazy.java | 35 ++
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 +-
.../variant/vcf/VCFContigHeaderLine.java | 2 +-
.../org/broadinstitute/variant/vcf/VCFEncoder.java | 381 ++++++++++++++
.../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 +-
.../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 +
.../empty.txt} | 0
.../illumina-sanger_full_range_as_sanger-62.fastq | 2 +-
.../sf/picard/sam/fastq2bam/ok-paired/pair1.txt | 2 +-
.../s_1_1_sequence.txt | 2 +-
.../s_1_2_sequence.txt | 3 +-
.../{fastq-illumina => ok-paired}/s_1_sequence.txt | 2 +-
.../{ok-paired => permissive-format}/pair1.txt | 5 +
.../{ok-paired => permissive-format}/pair2.txt | 8 +
.../s_1_1_sequence.txt | 11 +
.../s_1_2_sequence.txt | 1 +
.../s_1_sequence.txt | 22 +
212 files changed, 4968 insertions(+), 2978 deletions(-)
create mode 100644 src/c/inteldeflater/IntelDeflater.c
create mode 100644 src/java/net/sf/picard/fastq/Casava18ReadNameEncoder.java
create mode 100644 src/java/net/sf/picard/fastq/IlluminaReadNameEncoder.java
create mode 100644 src/java/net/sf/picard/fastq/ReadNameEncoder.java
create mode 100644 src/java/net/sf/samtools/seekablestream/ISeekableStreamFactory.java
create mode 100644 src/java/net/sf/samtools/util/Lazy.java
create mode 100644 src/java/net/sf/samtools/util/zip/DeflaterFactory.java
create mode 100644 src/java/net/sf/samtools/util/zip/IntelDeflater.java
create mode 100644 src/java/net/sf/samtools/util/zip/ZStreamRef.java
create mode 100644 src/java/org/broadinstitute/variant/vcf/VCFEncoder.java
create mode 100644 src/java/org/broadinstitute/variant/vcf/VCFRecordCodec.java
create mode 100644 src/scripts/build_intel_deflater.sh
create mode 100644 src/tests/java/net/sf/picard/util/MathUtilTest.java
create mode 100644 src/tests/java/org/broadinstitute/variant/vcf/VCFEncoderTest.java
create mode 100644 testdata/net/sf/picard/io/5newline5.txt
copy testdata/net/sf/picard/{illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => io/empty.txt} (100%)
copy testdata/net/sf/picard/sam/fastq2bam/{fastq-illumina => ok-paired}/illumina-sanger_full_range_as_sanger-62.fastq (69%)
copy testdata/net/sf/picard/sam/fastq2bam/{fastq-illumina => ok-paired}/s_1_1_sequence.txt (99%)
copy testdata/net/sf/picard/sam/fastq2bam/{fastq-illumina => ok-paired}/s_1_2_sequence.txt (99%)
copy testdata/net/sf/picard/sam/fastq2bam/{fastq-illumina => ok-paired}/s_1_sequence.txt (99%)
copy testdata/net/sf/picard/sam/fastq2bam/{ok-paired => permissive-format}/pair1.txt (97%)
copy testdata/net/sf/picard/sam/fastq2bam/{ok-paired => permissive-format}/pair2.txt (96%)
copy testdata/net/sf/picard/sam/fastq2bam/{fastq-illumina => permissive-format}/s_1_1_sequence.txt (99%)
copy testdata/net/sf/picard/sam/fastq2bam/{fastq-illumina => permissive-format}/s_1_2_sequence.txt (99%)
copy testdata/net/sf/picard/sam/fastq2bam/{fastq-illumina => permissive-format}/s_1_sequence.txt (98%)
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