[med-svn] [picard-tools] branch master updated (0ac9d98 -> ddb817f)
Charles Plessy
plessy at moszumanska.debian.org
Sun Apr 6 02:31:53 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository picard-tools.
from 0ac9d98 Merge branch 'upstream'
new ad4ec03 Imported Upstream version 1.110
new e87bdf5 Merge tag 'upstream/1.110'
new a11c89b New upstream release, with no new copyright nor license notices.
new 3e74739 Normalised with config-model-edit.
new 33d232d Refreshed patch for upstream version 1.110.
new ddb817f picard-tools (1.110-1) unstable; urgency=medium
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:
Picard-public.ipr | 20 +-
build.xml | 2 +-
debian/changelog | 8 +
debian/control | 44 +-
debian/copyright | 2 +-
debian/patches/use_libjbzip2-java | 8 +-
.../net/sf/picard/analysis/InsertSizeMetrics.java | 2 +-
.../directed/InsertSizeMetricsCollector.java | 2 +-
src/java/net/sf/picard/fastq/BasicFastqWriter.java | 3 +-
src/java/net/sf/picard/fastq/FastqReader.java | 11 +-
.../net/sf/picard/filter/FilteringIterator.java | 2 +-
.../sf/picard/illumina/CheckIlluminaDirectory.java | 161 ++--
.../picard/illumina/ExtractIlluminaBarcodes.java | 11 +-
.../illumina/IlluminaBasecallsConverter.java | 14 +-
.../picard/illumina/IlluminaBasecallsToFastq.java | 5 +-
.../sf/picard/illumina/IlluminaBasecallsToSam.java | 8 +-
.../net/sf/picard/illumina/parser/BclParser.java | 14 +-
.../parser/IlluminaDataProviderFactory.java | 22 +-
.../picard/illumina/parser/IlluminaFileUtil.java | 683 ++++++++++----
.../illumina/parser/IlluminaMetricsCode.java | 42 +
.../picard/illumina/parser/MultiTileBclParser.java | 2 +-
.../illumina/parser/PerTilePerCycleParser.java | 4 +-
src/java/net/sf/picard/illumina/parser/Tile.java | 114 +++
.../net/sf/picard/illumina/parser/TileIndex.java | 3 +-
.../sf/picard/illumina/parser/TileMetricsUtil.java | 162 ++--
.../picard/illumina/parser/TilePhasingValue.java | 30 +
.../parser/TileTemplateRead.java} | 14 +-
.../illumina/parser/fakers/BarcodeFileFaker.java | 25 +
.../illumina/parser/fakers/BciFileFaker.java | 52 ++
.../illumina/parser/fakers/BclFileFaker.java | 29 +
.../illumina/parser/fakers/CifFileFaker.java | 31 +
.../illumina/parser/fakers/ClocsFileFaker.java | 25 +
.../illumina/parser/fakers/CnfFileFaker.java | 31 +
.../picard/illumina/parser/fakers/FileFaker.java | 73 ++
.../illumina/parser/fakers/FilterFileFaker.java | 26 +
.../illumina/parser/fakers/LocsFileFaker.java | 28 +
.../parser/fakers/MultiTileBclFileFaker.java | 32 +
.../parser/fakers/MultiTileLocsFileFaker.java | 30 +
.../illumina/parser/fakers/PosFileFaker.java | 25 +
.../illumina/parser/fakers/QSeqFileFaker.java | 25 +
.../picard/illumina/parser/readers/BclReader.java | 67 +-
.../parser/readers/TileMetricsOutReader.java | 82 +-
src/java/net/sf/picard/io/IoUtil.java | 25 +-
.../net/sf/picard/sam/AbstractAlignmentMerger.java | 48 +-
src/java/net/sf/picard/sam/FastqToSam.java | 5 +-
src/java/net/sf/picard/sam/MergeBamAlignment.java | 9 +-
...RevertOriginalBaseQualitiesAndAddMateCigar.java | 2 +-
src/java/net/sf/picard/sam/SamAlignmentMerger.java | 16 +-
src/java/net/sf/picard/sam/SamFileValidator.java | 4 +-
src/java/net/sf/picard/sam/ValidateSamFile.java | 1 +
src/java/net/sf/picard/util/IntervalList.java | 4 +-
src/java/net/sf/picard/util/MathUtil.java | 13 +
src/java/net/sf/picard/util/OverlapDetector.java | 24 +-
.../sf/picard/util/QualityEncodingDetector.java | 110 ++-
src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 47 +-
src/java/net/sf/samtools/AbstractBAMFileIndex.java | 53 +-
src/java/net/sf/samtools/BAMFileReader.java | 11 +-
src/java/net/sf/samtools/BAMIndexContent.java | 156 +---
src/java/net/sf/samtools/BAMIndexer.java | 186 ++--
src/java/net/sf/samtools/Bin.java | 16 +-
src/java/net/sf/samtools/BinaryBAMIndexWriter.java | 20 +-
src/java/net/sf/samtools/BinningIndexBuilder.java | 187 ++++
...MIndexContent.java => BinningIndexContent.java} | 465 +++++-----
src/java/net/sf/samtools/CachingBAMFileIndex.java | 28 +-
src/java/net/sf/samtools/Chunk.java | 6 +-
src/java/net/sf/samtools/Defaults.java | 11 +
src/java/net/sf/samtools/GenomicIndexUtil.java | 100 +++
src/java/net/sf/samtools/LinearIndex.java | 30 +-
src/java/net/sf/samtools/SAMFileReader.java | 10 +-
src/java/net/sf/samtools/SAMFileWriterFactory.java | 6 +-
src/java/net/sf/samtools/SAMRecord.java | 13 +-
src/java/net/sf/samtools/SAMRecordSetBuilder.java | 185 +++-
src/java/net/sf/samtools/SAMUtils.java | 35 +-
.../sf/{picard/sam => samtools}/SamPairUtil.java | 43 +-
.../net/sf/samtools/TextualBAMIndexWriter.java | 12 +-
.../seekablestream/SeekableStreamFactory.java | 3 +-
src/java/net/sf/samtools/util/AsciiWriter.java | 4 +-
.../samtools/util/BlockCompressedInputStream.java | 9 +-
.../samtools/util/BlockCompressedOutputStream.java | 25 +-
.../net/sf/samtools/util/BufferedLineReader.java | 4 +-
src/java/net/sf/samtools/util/IOUtil.java | 81 +-
.../sf/samtools/util}/LocationAware.java | 6 +-
.../net/sf/samtools/util/SortingCollection.java | 6 +-
.../sf/samtools/util/SortingLongCollection.java | 4 +-
.../net/sf/samtools/util/TempStreamFactory.java | 16 +-
.../org/broad/tribble/AbstractFeatureReader.java | 3 +-
src/java/org/broad/tribble/AsciiFeatureCodec.java | 1 +
src/java/org/broad/tribble/BinaryFeatureCodec.java | 4 +-
src/java/org/broad/tribble/FeatureCodec.java | 2 +-
.../broad/tribble/TribbleIndexedFeatureReader.java | 75 +-
.../org/broad/tribble/index/AbstractIndex.java | 115 ++-
src/java/org/broad/tribble/index/Block.java | 14 +-
.../broad/tribble/index/DynamicIndexCreator.java | 83 +-
src/java/org/broad/tribble/index/Index.java | 36 +-
src/java/org/broad/tribble/index/IndexCreator.java | 25 -
src/java/org/broad/tribble/index/IndexFactory.java | 202 +++--
.../broad/tribble/index/MutableIndex.java} | 26 +-
.../broad/tribble/index/TribbleIndexCreator.java} | 27 +-
.../index/interval/IntervalIndexCreator.java | 46 +-
.../tribble/index/interval/IntervalTreeIndex.java | 66 +-
.../broad/tribble/index/linear/LinearIndex.java | 127 +--
.../tribble/index/linear/LinearIndexCreator.java | 25 +-
.../org/broad/tribble/index/tabix/TabixFormat.java | 109 +++
.../org/broad/tribble/index/tabix/TabixIndex.java | 364 ++++++++
.../tribble/index/tabix/TabixIndexCreator.java | 199 ++++
.../org/broad/tribble/readers/AsciiLineReader.java | 23 +-
.../tribble/readers/AsciiLineReaderIterator.java | 5 +-
.../tribble/readers/AsynchronousLineReader.java | 9 +-
src/java/org/broad/tribble/readers/Positional.java | 2 +
.../org/broad/tribble/readers/TabixReader.java | 3 +-
.../writer/IndexingVariantContextWriter.java | 60 +-
.../writer/VariantContextWriterFactory.java | 55 +-
.../picard/analysis/CollectRnaSeqMetricsTest.java | 1 +
.../illumina/CheckIlluminaDirectoryTest.java | 304 ++++---
.../illumina/parser/TileMetricsUtilTest.java | 999 ---------------------
.../illumina/parser/readers/BclReaderTest.java | 8 +-
src/tests/java/net/sf/picard/sam/CleanSamTest.java | 24 +-
.../java/net/sf/picard/sam/MarkDuplicatesTest.java | 171 ++++
.../net/sf/picard/sam/MergeBamAlignmentTest.java | 24 +-
...MergingSamRecordIteratorGroupCollisionTest.java | 10 +-
.../net/sf/picard/sam/ValidateSamFileTest.java | 10 +-
.../net/sf/picard/sam/testers/CleanSamTester.java | 52 ++
.../picard/sam/testers/MarkDuplicatesTester.java | 55 ++
.../net/sf/picard/sam/testers/SamFileTester.java | 213 +++++
.../picard/util/QualityEncodingDetectorTest.java | 40 +-
.../java/net/sf/samtools/BAMFileIndexTest.java | 35 +
.../java/net/sf/samtools/BAMFileWriterTest.java | 2 -
.../{picard/sam => samtools}/SamPairUtilTest.java | 3 +-
.../java/org/broad/tribble/FeatureReaderTest.java | 2 +-
.../tribble/index/linear/LinearIndexTest.java | 44 +-
.../broad/tribble/index/tabix/TabixIndexTest.java | 65 ++
.../writer/TabixOnTheFlyIndexCreationTest.java | 66 ++
.../variantcontext/writer/VCFWriterUnitTest.java | 118 +--
.../HiSeq2000TileMetricsOut.bin | Bin 115202 -> 0 bytes
.../HiSeq2500TileMetricsOut.bin | Bin 19202 -> 0 bytes
.../TileMetricsUtilTest/MiSeqTileMetricsOut.bin | Bin 2942 -> 0 bytes
testdata/tribble/tabix/bigger.vcf.gz.tbi | Bin 0 -> 595996 bytes
testdata/variant/ex2.bgzf.bcf | Bin 0 -> 1062 bytes
testdata/variant/ex2.bgzf.bcf.csi | Bin 0 -> 130 bytes
testdata/variant/ex2.uncompressed.bcf | Bin 0 -> 1892 bytes
140 files changed, 5092 insertions(+), 2873 deletions(-)
create mode 100644 src/java/net/sf/picard/illumina/parser/IlluminaMetricsCode.java
create mode 100644 src/java/net/sf/picard/illumina/parser/Tile.java
create mode 100644 src/java/net/sf/picard/illumina/parser/TilePhasingValue.java
copy src/java/net/sf/picard/{fastq/FastqConstants.java => illumina/parser/TileTemplateRead.java} (81%)
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/BarcodeFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/BciFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/BclFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/CifFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/ClocsFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/CnfFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/FileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/FilterFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/LocsFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/MultiTileBclFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/MultiTileLocsFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/PosFileFaker.java
create mode 100644 src/java/net/sf/picard/illumina/parser/fakers/QSeqFileFaker.java
create mode 100644 src/java/net/sf/samtools/BinningIndexBuilder.java
copy src/java/net/sf/samtools/{BAMIndexContent.java => BinningIndexContent.java} (60%)
create mode 100644 src/java/net/sf/samtools/GenomicIndexUtil.java
rename src/java/net/sf/{picard/sam => samtools}/SamPairUtil.java (89%)
rename src/java/{org/broad/tribble/readers => net/sf/samtools/util}/LocationAware.java (79%)
copy src/java/{net/sf/samtools/util/ProgressLoggerInterface.java => org/broad/tribble/index/MutableIndex.java} (73%)
copy src/java/{net/sf/samtools/util/ProgressLoggerInterface.java => org/broad/tribble/index/TribbleIndexCreator.java} (73%)
create mode 100644 src/java/org/broad/tribble/index/tabix/TabixFormat.java
create mode 100644 src/java/org/broad/tribble/index/tabix/TabixIndex.java
create mode 100644 src/java/org/broad/tribble/index/tabix/TabixIndexCreator.java
delete mode 100644 src/tests/java/net/sf/picard/illumina/parser/TileMetricsUtilTest.java
create mode 100644 src/tests/java/net/sf/picard/sam/testers/CleanSamTester.java
create mode 100644 src/tests/java/net/sf/picard/sam/testers/MarkDuplicatesTester.java
create mode 100644 src/tests/java/net/sf/picard/sam/testers/SamFileTester.java
rename src/tests/java/net/sf/{picard/sam => samtools}/SamPairUtilTest.java (99%)
create mode 100644 src/tests/java/org/broad/tribble/index/tabix/TabixIndexTest.java
create mode 100644 src/tests/java/org/broadinstitute/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java
delete mode 100755 testdata/net/sf/picard/illumina/parser/TileMetricsUtilTest/HiSeq2000TileMetricsOut.bin
delete mode 100755 testdata/net/sf/picard/illumina/parser/TileMetricsUtilTest/HiSeq2500TileMetricsOut.bin
delete mode 100755 testdata/net/sf/picard/illumina/parser/TileMetricsUtilTest/MiSeqTileMetricsOut.bin
create mode 100644 testdata/tribble/tabix/bigger.vcf.gz.tbi
create mode 100755 testdata/variant/ex2.bgzf.bcf
create mode 100755 testdata/variant/ex2.bgzf.bcf.csi
create mode 100755 testdata/variant/ex2.uncompressed.bcf
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