[med-svn] [picard-tools] branch upstream updated (c38e07e -> d02872e)
Charles Plessy
plessy at alioth.debian.org
Sun Oct 20 01:39:09 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch upstream
in repository picard-tools.
from c38e07e Imported Upstream version 1.95
new d02872e Imported Upstream version 1.100
The 1 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 +-
.../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 +++++++
197 files changed, 4163 insertions(+), 1506 deletions(-)
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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