[med-svn] [picard-tools] branch master updated (53b7a12 -> 9232c97)
Charles Plessy
plessy at alioth.debian.org
Sun Oct 20 01:39:06 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository picard-tools.
from 53b7a12 set history of changes
new c5bf5d4 Compress the source archive with XZ.
new 4d81451 Mark the use of git-buildpackage and pristine-tar with a gbp.conf file.
new d02872e Imported Upstream version 1.100
new 2a7549d Merge tag 'upstream/1.100'
new 9232c97 New upstream release, no new copyright nor license file.
The 5 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.iml | 8 +-
Picard-public.ipr | 17 +
build.xml | 21 +-
debian/changelog | 8 +
debian/copyright | 2 +-
debian/gbp.conf | 5 +
debian/rules | 4 +-
.../analysis/AlignmentSummaryMetricsCollector.java | 4 +-
.../analysis/CollectAlignmentSummaryMetrics.java | 2 +-
.../picard/analysis/CollectInsertSizeMetrics.java | 2 +-
.../sf/picard/analysis/CollectMultipleMetrics.java | 2 +-
.../sf/picard/analysis/CollectRnaSeqMetrics.java | 1 +
.../net/sf/picard/analysis/MeanQualityByCycle.java | 2 +-
.../picard/analysis/QualityScoreDistribution.java | 2 +-
.../analysis/directed/CollectTargetedMetrics.java | 3 +-
.../directed/InsertSizeMetricsCollector.java | 2 +-
.../analysis/directed/RnaSeqMetricsCollector.java | 2 +-
.../analysis/directed/TargetMetricsCollector.java | 2 +-
.../net/sf/picard/cmdline/CommandLineParser.java | 2 +-
src/java/net/sf/picard/filter/ReadNameFilter.java | 35 +-
.../filter/SecondaryOrSupplementaryFilter.java | 32 ++
.../picard/illumina/ExtractIlluminaBarcodes.java | 16 +-
.../illumina/IlluminaBasecallsConverter.java | 14 +-
.../picard/illumina/IlluminaBasecallsToFastq.java | 13 +-
.../sf/picard/illumina/IlluminaBasecallsToSam.java | 14 +-
.../sf/picard/illumina/MarkIlluminaAdapters.java | 235 ++++++++++
.../sf/picard/illumina/parser/BarcodeParser.java | 2 +-
.../net/sf/picard/illumina/parser/BclParser.java | 16 +-
.../net/sf/picard/illumina/parser/CifParser.java | 2 +-
.../net/sf/picard/illumina/parser/CnfParser.java | 2 +-
.../sf/picard/illumina/parser/FilterParser.java | 2 +-
.../parser/IlluminaDataProviderFactory.java | 12 +-
.../picard/illumina/parser/IlluminaFileUtil.java | 4 +-
.../illumina/parser/IlluminaIntensityParser.java | 2 +-
.../illumina/parser/PerTilePerCycleParser.java | 6 +-
.../net/sf/picard/illumina/parser/PosParser.java | 2 +-
.../net/sf/picard/illumina/parser/QseqParser.java | 1 +
.../sf/picard/illumina/parser/TileMetricsUtil.java | 2 +-
.../readers/BclQualityEvaluationStrategy.java | 95 ++++
.../picard/illumina/parser/readers/BclReader.java | 11 +-
src/java/net/sf/picard/io/IoUtil.java | 114 ++++-
.../picard/reference/IndexedFastaSequenceFile.java | 12 +-
.../net/sf/picard/sam/AbstractAlignmentMerger.java | 51 +-
.../sam/AbstractDuplicateFindingAlgorithm.java | 5 +-
.../net/sf/picard/sam/AddOrReplaceReadGroups.java | 5 +-
src/java/net/sf/picard/sam/CompareSAMs.java | 18 +-
src/java/net/sf/picard/sam/DownsampleSam.java | 2 +-
src/java/net/sf/picard/sam/FastqToSam.java | 4 +-
src/java/net/sf/picard/sam/FixMateInformation.java | 4 +-
src/java/net/sf/picard/sam/HitsForInsert.java | 25 +-
src/java/net/sf/picard/sam/MarkDuplicates.java | 4 +-
src/java/net/sf/picard/sam/MergeBamAlignment.java | 6 +-
src/java/net/sf/picard/sam/MergeSamFiles.java | 2 +-
...stDistantPrimaryAlignmentSelectionStrategy.java | 2 +-
.../sf/picard/sam/MultiHitAlignedReadIterator.java | 25 +-
src/java/net/sf/picard/sam/RevertSam.java | 3 +-
src/java/net/sf/picard/sam/SamAlignmentMerger.java | 3 +-
src/java/net/sf/picard/sam/SamFileValidator.java | 2 +-
src/java/net/sf/picard/sam/SamToFastq.java | 2 +-
.../net/sf/picard/util/AbstractInputParser.java | 1 +
src/java/net/sf/picard/util/CsvInputParser.java | 36 ++
.../util/DelimitedTextFileWithHeaderIterator.java | 111 +++++
src/java/net/sf/picard/util/IntervalTreeMap.java | 3 +-
src/java/net/sf/picard/util/IterableAdapter.java | 29 ++
.../net/sf/picard/util/IterableOnceIterator.java | 42 ++
src/java/net/sf/picard/util/MathUtil.java | 11 +-
src/java/net/sf/picard/util/ProcessExecutor.java | 60 +++
src/java/net/sf/picard/util/RExecutor.java | 1 +
src/java/net/sf/picard/util/SamLocusIterator.java | 2 +-
src/java/net/sf/picard/util/TabbedInputParser.java | 3 +-
.../util/TabbedTextFileWithHeaderParser.java | 1 -
src/java/net/sf/picard/vcf/BcfIterator.java | 84 ----
src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 90 ++++
src/java/net/sf/picard/vcf/MergeVcfs.java | 55 ++-
src/java/net/sf/picard/vcf/SplitVcfs.java | 59 ++-
.../net/sf/picard/vcf/VariantContextIterator.java | 34 --
.../picard/vcf/VariantContextIteratorFactory.java | 49 --
.../net/sf/picard/vcf/VariantContextUtils.java | 64 ---
src/java/net/sf/picard/vcf/VcfFormatConverter.java | 54 ++-
src/java/net/sf/picard/vcf/VcfIterator.java | 92 ----
src/java/net/sf/samtools/SAMFileReader.java | 17 +-
src/java/net/sf/samtools/SAMRecord.java | 56 ++-
.../sf/samtools/SAMRecordQueryNameComparator.java | 3 +
src/java/net/sf/samtools/SAMSequenceRecord.java | 2 +-
src/java/net/sf/samtools/SAMValidationError.java | 3 +
.../SecondaryOrSupplementarySkippingIterator.java | 41 ++
.../seekablestream/SeekableStreamFactory.java | 9 +
.../util/AbstractIterator.java | 16 +-
src/java/net/sf/samtools/util/BinaryCodec.java | 3 +-
.../net/sf/samtools/util/BufferedLineReader.java | 2 +
.../{picard => samtools}/util/CollectionUtil.java | 14 +-
src/java/net/sf/samtools/util/Tuple.java | 16 +
.../org/broad/tribble/AbstractFeatureCodec.java | 16 +-
.../org/broad/tribble/AbstractFeatureReader.java | 29 +-
src/java/org/broad/tribble/AsciiFeatureCodec.java | 108 ++---
src/java/org/broad/tribble/BinaryFeatureCodec.java | 42 ++
.../broad/tribble/CloseableTribbleIterator.java | 8 +-
src/java/org/broad/tribble/FeatureCodec.java | 93 ++--
src/java/org/broad/tribble/TabixFeatureReader.java | 38 +-
.../broad/tribble/TribbleIndexedFeatureReader.java | 190 +++++---
src/java/org/broad/tribble/bed/BEDCodec.java | 15 +-
.../org/broad/tribble/dbsnp/OldDbSNPCodec.java | 8 +-
.../broad/tribble/example/ExampleBinaryCodec.java | 27 +-
.../org/broad/tribble/gelitext/GeliTextCodec.java | 68 +--
src/java/org/broad/tribble/index/IndexFactory.java | 93 ++--
.../org/broad/tribble/readers/AsciiLineReader.java | 25 +-
.../tribble/readers/AsciiLineReaderIterator.java | 99 ++++
.../tribble/readers/AsynchronousLineReader.java | 97 ++++
.../org/broad/tribble/readers/LineIterator.java | 12 +
.../broad/tribble/readers/LineIteratorImpl.java | 33 ++
.../org/broad/tribble/readers/LineReaderUtil.java | 61 +++
.../org/broad/tribble/readers/LocationAware.java | 24 +
.../tribble/readers/LongLineBufferedReader.java | 490 ++++++++++++++++++++
src/java/org/broad/tribble/readers/Positional.java | 20 +-
.../tribble/readers/PositionalBufferedStream.java | 13 +-
.../tribble/readers/TabixIteratorLineReader.java | 8 +-
src/java/org/broad/tribble/util/IOUtil.java | 66 ---
.../org/broadinstitute/variant/bcf2/BCF2Codec.java | 14 +-
.../org/broadinstitute/variant/bcf2/BCF2Utils.java | 2 +-
.../variant/variantcontext/VariantContext.java | 16 +-
.../variantcontext}/VariantContextComparator.java | 3 +-
.../writer/IndexingVariantContextWriter.java | 8 +-
.../variant/variantcontext/writer/VCFWriter.java | 16 +-
.../writer/VariantContextWriterFactory.java | 6 +-
.../variant/vcf/AbstractVCFCodec.java | 9 +-
.../org/broadinstitute/variant/vcf/VCF3Codec.java | 62 ++-
.../org/broadinstitute/variant/vcf/VCFCodec.java | 70 ++-
.../broadinstitute/variant/vcf/VCFConstants.java | 1 +
.../variant/vcf/VCFContigHeaderLine.java | 38 +-
.../broadinstitute/variant/vcf/VCFFileReader.java | 69 +++
.../variant/vcf/VCFFilterHeaderLine.java | 5 +
.../variant/vcf/VCFFormatHeaderLine.java | 5 +
.../org/broadinstitute/variant/vcf/VCFHeader.java | 63 ++-
.../broadinstitute/variant/vcf/VCFHeaderLine.java | 10 +-
.../variant/vcf/VCFInfoHeaderLine.java | 5 +
.../variant/vcf/VCFSimpleHeaderLine.java | 12 +-
src/scripts/explain_sam_flags.py | 3 +-
.../net/sf/picard/analysis/insertSizeHistogram.R | 108 ++---
.../net/sf/picard/analysis/rnaSeqCoverage.R | 18 +-
src/scripts/release_picard.sh | 6 +
.../picard/analysis/MultiLevelCollectorTest.java | 2 +-
.../sf/picard/cmdline/CommandLineParserTest.java | 2 +-
.../illumina/CheckIlluminaDirectoryTest.java | 2 +-
.../illumina/ExtractIlluminaBarcodesTest.java | 4 +-
.../net/sf/picard/illumina/ReadStructureTest.java | 5 +-
.../sf/picard/illumina/parser/BclParserTest.java | 5 +-
.../net/sf/picard/illumina/parser/BinTdUtil.java | 2 +-
.../illumina/parser/CycleIlluminaFileMapTest.java | 2 +-
.../parser/IlluminaDataProviderFactoryTest.java | 4 +-
.../illumina/parser/IlluminaDataProviderTest.java | 13 +-
.../illumina/parser/IlluminaFileUtilTest.java | 2 +-
.../picard/illumina/parser/PerTileParserTest.java | 2 +-
.../illumina/parser/PerTilePerCycleParserTest.java | 3 +-
.../sf/picard/illumina/parser/PosParserTest.java | 2 +-
.../sf/picard/illumina/parser/QseqParserTest.java | 2 +-
.../illumina/parser/readers/BclReaderTest.java | 159 +++++--
src/tests/java/net/sf/picard/io/IoUtilTest.java | 15 +
.../net/sf/picard/sam/MergeBamAlignmentTest.java | 83 +++-
...> DelimitedTextFileWithHeaderIteratorTest.java} | 28 +-
...RExecutorTest.java => IntervalTreeMapTest.java} | 31 +-
.../net/sf/picard/util/SamLocusIteratorTest.java | 2 -
.../java/net/sf/picard/vcf/MergeVcfsTest.java | 88 ++--
.../java/net/sf/picard/vcf/SplitVcfsTest.java | 35 +-
.../picard/vcf/VariantContextComparatorTest.java | 1 +
.../sf/picard/vcf/VariantContextIteratorTest.java | 24 -
.../net/sf/picard/vcf/VcfFormatConverterTest.java | 62 +--
.../seekablestream/SeekableStreamFactoryTest.java | 15 +
.../broad/tribble/AbstractFeatureReaderTest.java | 39 +-
.../java/org/broad/tribble/BinaryFeaturesTest.java | 9 +-
.../java/org/broad/tribble/FeatureReaderTest.java | 51 +-
.../org/broad/tribble/index/IndexFactoryTest.java | 3 +-
.../tribble/index/interval/IntervalTreeTest.java | 2 +-
.../readers/AsynchronousLineReaderTest.java | 31 ++
.../broad/tribble/readers/LineReaderUtilTest.java | 27 ++
.../readers/LongLineBufferedReaderTest.java | 33 ++
.../java/org/broad/tribble/readers/ReaderTest.java | 7 +-
.../variant/bcf2/BCF2UtilsUnitTest.java | 30 ++
.../variantcontext/VariantContextTestProvider.java | 108 +++--
.../variantcontext/VariantContextUnitTest.java | 36 +-
.../variantcontext/writer/VCFWriterUnitTest.java | 51 +-
.../writer/VariantContextWritersUnitTest.java | 27 +-
.../variant/vcf/IndexFactoryUnitTest.java | 6 +-
.../variant/vcf/VCFHeaderUnitTest.java | 6 +-
testdata/net/sf/picard/io/slurptest.txt | 3 +
.../aligned.supplement.sam} | 2 +
.../picard/vcf/CEUTrio-indels-bad-samples.vcf.idx | Bin 0 -> 15212 bytes
.../vcf/CEUTrio-indels-dissimilar-contigs.vcf.idx | Bin 0 -> 13460 bytes
testdata/net/sf/picard/vcf/CEUTrio-indels.vcf.idx | Bin 0 -> 15200 bytes
.../picard/vcf/CEUTrio-merged-indels-snps.vcf.idx | Bin 0 -> 26611 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-0.vcf.idx | Bin 0 -> 17156 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-1.vcf.idx | Bin 0 -> 18707 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-2.vcf.idx | Bin 0 -> 18693 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-3.vcf.idx | Bin 0 -> 14381 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-4.vcf.idx | Bin 0 -> 14620 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-5.vcf.idx | Bin 0 -> 15823 bytes
testdata/net/sf/picard/vcf/CEUTrio-snps.vcf.idx | Bin 0 -> 26434 bytes
testdata/net/sf/picard/vcf/vcfFormatTest.bcf | Bin 28266 -> 86444 bytes
testdata/net/sf/picard/vcf/vcfFormatTest.bcf.idx | Bin 0 -> 26598 bytes
testdata/net/sf/picard/vcf/vcfFormatTest.vcf | 264 +++++++++++
testdata/net/sf/picard/vcf/vcfFormatTest.vcf.idx | Bin 0 -> 26586 bytes
testdata/tribble/large.txt | 165 +++++++
201 files changed, 4179 insertions(+), 1509 deletions(-)
create mode 100644 debian/gbp.conf
create mode 100644 src/java/net/sf/picard/filter/SecondaryOrSupplementaryFilter.java
create mode 100644 src/java/net/sf/picard/illumina/MarkIlluminaAdapters.java
create mode 100644 src/java/net/sf/picard/illumina/parser/readers/BclQualityEvaluationStrategy.java
create mode 100644 src/java/net/sf/picard/util/CsvInputParser.java
create mode 100644 src/java/net/sf/picard/util/DelimitedTextFileWithHeaderIterator.java
create mode 100644 src/java/net/sf/picard/util/IterableAdapter.java
create mode 100644 src/java/net/sf/picard/util/IterableOnceIterator.java
delete mode 100644 src/java/net/sf/picard/vcf/BcfIterator.java
create mode 100644 src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java
delete mode 100644 src/java/net/sf/picard/vcf/VariantContextIterator.java
delete mode 100644 src/java/net/sf/picard/vcf/VariantContextIteratorFactory.java
delete mode 100644 src/java/net/sf/picard/vcf/VariantContextUtils.java
delete mode 100644 src/java/net/sf/picard/vcf/VcfIterator.java
create mode 100644 src/java/net/sf/samtools/SecondaryOrSupplementarySkippingIterator.java
rename src/java/net/sf/{picard => samtools}/util/AbstractIterator.java (85%)
rename src/java/net/sf/{picard => samtools}/util/CollectionUtil.java (94%)
create mode 100644 src/java/net/sf/samtools/util/Tuple.java
create mode 100644 src/java/org/broad/tribble/BinaryFeatureCodec.java
create mode 100644 src/java/org/broad/tribble/readers/AsciiLineReaderIterator.java
create mode 100644 src/java/org/broad/tribble/readers/AsynchronousLineReader.java
create mode 100644 src/java/org/broad/tribble/readers/LineIterator.java
create mode 100644 src/java/org/broad/tribble/readers/LineIteratorImpl.java
create mode 100644 src/java/org/broad/tribble/readers/LineReaderUtil.java
create mode 100644 src/java/org/broad/tribble/readers/LocationAware.java
create mode 100644 src/java/org/broad/tribble/readers/LongLineBufferedReader.java
delete mode 100644 src/java/org/broad/tribble/util/IOUtil.java
rename src/java/{net/sf/picard/vcf => org/broadinstitute/variant/variantcontext}/VariantContextComparator.java (97%)
create mode 100644 src/java/org/broadinstitute/variant/vcf/VCFFileReader.java
copy src/tests/java/net/sf/picard/util/{TabbedTextFileWithHeaderParserTest.java => DelimitedTextFileWithHeaderIteratorTest.java} (73%)
copy src/tests/java/net/sf/picard/util/{RExecutorTest.java => IntervalTreeMapTest.java} (64%)
mode change 100755 => 100644
delete mode 100644 src/tests/java/net/sf/picard/vcf/VariantContextIteratorTest.java
create mode 100644 src/tests/java/net/sf/samtools/seekablestream/SeekableStreamFactoryTest.java
create mode 100644 src/tests/java/org/broad/tribble/readers/AsynchronousLineReaderTest.java
create mode 100644 src/tests/java/org/broad/tribble/readers/LineReaderUtilTest.java
create mode 100644 src/tests/java/org/broad/tribble/readers/LongLineBufferedReaderTest.java
create mode 100644 testdata/net/sf/picard/io/slurptest.txt
copy testdata/net/sf/picard/sam/{aligned_queryname_sorted.sam => MergeBamAlignment/aligned.supplement.sam} (81%)
mode change 100755 => 100644
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-indels-bad-samples.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-indels.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-merged-indels-snps.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-random-scatter-0.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-random-scatter-1.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-random-scatter-2.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-random-scatter-3.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-random-scatter-4.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-random-scatter-5.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/CEUTrio-snps.vcf.idx
create mode 100644 testdata/net/sf/picard/vcf/vcfFormatTest.bcf.idx
create mode 100644 testdata/net/sf/picard/vcf/vcfFormatTest.vcf.idx
create mode 100644 testdata/tribble/large.txt
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