[med-svn] [htsjdk] 03/06: Merge tag 'upstream/2.0.1+dfsg.1'
Andreas Tille
tille at debian.org
Sat Dec 19 21:26:57 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository htsjdk.
commit 19b7536927765b6730be5704d88816fb5a6b14b6
Merge: 800d414 ad6800c
Author: Andreas Tille <tille at debian.org>
Date: Sat Dec 19 21:26:32 2015 +0100
Merge tag 'upstream/2.0.1+dfsg.1'
Upstream version 2.0.1+dfsg.1
.idea/modules/htsjdk.iml | 3 +-
.travis.yml | 5 +-
README.md | 2 +
build.sbt | 8 +-
build.xml | 9 +-
htsjdk.iml | 9 +
src/java/htsjdk/samtools/AbstractBAMFileIndex.java | 27 +-
.../{SAMFileSpan.java => BAMFileSpan.java} | 59 +-
src/java/htsjdk/samtools/BAMRecord.java | 7 +-
src/java/htsjdk/samtools/BAMRecordCodec.java | 6 +-
src/java/htsjdk/samtools/BinaryTagCodec.java | 11 +-
src/java/htsjdk/samtools/CRAMFileReader.java | 64 +-
src/java/htsjdk/samtools/CRAMFileWriter.java | 99 +-
src/java/htsjdk/samtools/CRAMIndexer.java | 36 +-
src/java/htsjdk/samtools/CRAMIterator.java | 34 +-
.../samtools/ChainedDownsamplingIterator.java | 90 ++
.../ConstantMemoryDownsamplingIterator.java | 88 ++
.../htsjdk/samtools/DefaultSAMRecordFactory.java | 6 +-
src/java/htsjdk/samtools/DownsamplingIterator.java | 164 ++-
.../samtools/DownsamplingIteratorFactory.java | 118 +++
.../htsjdk/samtools/DuplicateScoringStrategy.java | 39 +-
src/java/htsjdk/samtools/DuplicateSet.java | 70 +-
.../samtools/HighAccuracyDownsamplingIterator.java | 196 ++++
.../htsjdk/samtools/MergingSamRecordIterator.java | 12 +-
.../SAMBinaryTagAndUnsignedArrayValue.java | 14 +-
src/java/htsjdk/samtools/SAMBinaryTagAndValue.java | 43 +-
src/java/htsjdk/samtools/SAMFileSpan.java | 244 -----
src/java/htsjdk/samtools/SAMFileWriterFactory.java | 149 ++-
src/java/htsjdk/samtools/SAMFileWriterImpl.java | 20 +-
src/java/htsjdk/samtools/SAMRecord.java | 680 ++++++++++---
.../samtools/SAMRecordCoordinateComparator.java | 6 +
.../samtools/SAMRecordDuplicateComparator.java | 46 +-
.../samtools/SAMRecordQueryHashComparator.java | 68 ++
src/java/htsjdk/samtools/SAMTag.java | 3 +
src/java/htsjdk/samtools/SAMUtils.java | 174 +++-
src/java/htsjdk/samtools/SRAFileReader.java | 306 ++++++
src/java/htsjdk/samtools/SRAIndex.java | 257 +++++
src/java/htsjdk/samtools/SRAIterator.java | 248 +++++
src/java/htsjdk/samtools/SamFileValidator.java | 21 +-
src/java/htsjdk/samtools/SamFiles.java | 23 +-
src/java/htsjdk/samtools/SamIndexes.java | 94 ++
src/java/htsjdk/samtools/SamInputResource.java | 68 +-
src/java/htsjdk/samtools/SamPairUtil.java | 55 +-
src/java/htsjdk/samtools/SamReader.java | 1 +
src/java/htsjdk/samtools/SamReaderFactory.java | 47 +-
src/java/htsjdk/samtools/SamStreams.java | 1 +
src/java/htsjdk/samtools/TextTagCodec.java | 19 +-
src/java/htsjdk/samtools/cram/CRAIEntry.java | 148 +++
src/java/htsjdk/samtools/cram/CRAIIndex.java | 164 +++
src/java/htsjdk/samtools/cram/CRAMException.java | 22 +
.../samtools/cram/build/ContainerParser.java | 13 +-
src/java/htsjdk/samtools/cram/build/CramIO.java | 10 +-
.../samtools/cram/build/Sam2CramRecordFactory.java | 13 +
.../cram/encoding/reader/CramRecordReader.java | 22 +-
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 9 +-
.../cram/structure/CramCompressionRecord.java | 6 +-
.../htsjdk/samtools/cram/structure/ReadTag.java | 30 +-
.../htsjdk/samtools/filter/FilteringIterator.java | 2 +-
.../htsjdk/samtools/filter/IntervalFilter.java | 2 +-
.../samtools/filter/OverclippedReadFilter.java | 76 ++
src/java/htsjdk/samtools/metrics/MetricsFile.java | 32 +-
.../reference/AbstractFastaSequenceFile.java | 74 +-
.../samtools/reference/FastaSequenceFile.java | 18 +-
.../samtools/reference/FastaSequenceIndex.java | 21 +-
.../reference/IndexedFastaSequenceFile.java | 96 +-
.../reference/ReferenceSequenceFileFactory.java | 45 +-
.../seekablestream/SeekableMemoryStream.java | 64 ++
src/java/htsjdk/samtools/sra/ReferenceCache.java | 79 ++
src/java/htsjdk/samtools/sra/SRAAccession.java | 108 ++
.../htsjdk/samtools/sra/SRAAlignmentIterator.java | 194 ++++
.../samtools/sra/SRAIndexedSequenceFile.java | 121 +++
src/java/htsjdk/samtools/sra/SRALazyRecord.java | 1056 ++++++++++++++++++++
.../samtools/sra/SRAUnalignmentIterator.java | 181 ++++
src/java/htsjdk/samtools/sra/SRAUtils.java | 83 ++
.../htsjdk/samtools/util/AbstractAsyncWriter.java | 2 +-
.../samtools/util/AbstractProgressLogger.java | 2 +-
src/java/htsjdk/samtools/util/BinaryCodec.java | 10 +-
src/java/htsjdk/samtools/util/DiskBackedQueue.java | 12 +-
src/java/htsjdk/samtools/util/Histogram.java | 20 +-
src/java/htsjdk/samtools/util/IOUtil.java | 62 +-
src/java/htsjdk/samtools/util/Murmur3.java | 115 +++
src/java/htsjdk/samtools/util/ProgressLogger.java | 2 +-
src/java/htsjdk/samtools/util/SequenceUtil.java | 57 +-
src/java/htsjdk/samtools/util/StringUtil.java | 4 +-
.../variant/variantcontext/VariantContext.java | 8 +-
.../variantcontext/filter/CompoundFilter.java | 74 ++
.../variantcontext/filter/FilteringIterator.java | 127 +++
.../filter/GenotypeQualityFilter.java | 79 ++
.../filter/HeterozygosityFilter.java | 84 ++
.../filter/PassingVariantFilter.java} | 71 +-
.../variantcontext/filter/SnpFilter.java} | 71 +-
.../filter/VariantContextFilter.java} | 70 +-
.../variantcontext/writer/BCF2FieldEncoder.java | 35 +-
.../writer/VariantContextWriterBuilder.java | 25 +-
src/java/htsjdk/variant/vcf/VCFRecordCodec.java | 18 +-
.../java/htsjdk/samtools/BAMFileWriterTest.java | 133 ++-
.../java/htsjdk/samtools/CRAMComplianceTest.java | 7 +-
.../java/htsjdk/samtools/CRAMEdgeCasesTest.java | 33 +-
.../java/htsjdk/samtools/CRAMFileIndexTest.java | 66 ++
.../samtools/CRAMFileWriterWithIndexTest.java | 3 +-
src/tests/java/htsjdk/samtools/CigarTest.java | 81 +-
.../java/htsjdk/samtools/CramFileWriterTest.java | 122 ++-
.../htsjdk/samtools/DownsamplingIteratorTests.java | 82 ++
.../htsjdk/samtools/DuplicateSetIteratorTest.java | 5 +-
.../samtools/MergingSamRecordIteratorTest.java | 41 +
.../java/htsjdk/samtools/SAMFileReaderTest.java | 69 +-
.../htsjdk/samtools/SAMFileWriterFactoryTest.java | 159 ++-
.../java/htsjdk/samtools/SAMIntegerTagTest.java | 167 +++-
.../samtools/SAMRecordDuplicateComparatorTest.java | 15 +
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 797 ++++++++++++++-
.../java/htsjdk/samtools/SAMTextWriterTest.java | 12 +
src/tests/java/htsjdk/samtools/SAMUtilsTest.java | 106 ++
src/tests/java/htsjdk/samtools/SamFilesTest.java | 60 ++
src/tests/java/htsjdk/samtools/SamIndexesTest.java | 192 ++++
.../java/htsjdk/samtools/SamReaderFactoryTest.java | 25 +
src/tests/java/htsjdk/samtools/SamSpecIntTest.java | 4 +-
.../java/htsjdk/samtools/cram/CRAIEntryTest.java | 145 +++
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 133 +++
.../htsjdk/samtools/cram/build/CramIOTest.java | 82 ++
.../cram/structure/CramCompressionRecordTest.java | 68 ++
.../samtools/cram/structure/ReadTagTest.java | 21 +-
.../samtools/filter/OverclippedReadFilterTest.java | 83 ++
.../htsjdk/samtools/metrics/MetricsFileTest.java | 21 +
.../samtools/reference/FastaSequenceIndexTest.java | 8 +-
.../reference/IndexedFastaSequenceFileTest.java | 10 +-
.../java/htsjdk/samtools/sra/SRAIndexTest.java | 150 +++
.../htsjdk/samtools/sra/SRALazyRecordTest.java | 51 +
.../java/htsjdk/samtools/sra/SRAQueryTest.java | 116 +++
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 25 +
src/tests/java/htsjdk/samtools/sra/SRATest.java | 464 +++++++++
.../java/htsjdk/samtools/util/CodeUtilTest.java | 2 +-
.../htsjdk/samtools/util/DiskBackedQueueTest.java | 30 +-
.../htsjdk/samtools/util/SequenceUtilTest.java | 22 +
.../samtools/util/SortingCollectionTest.java | 39 +-
.../htsjdk/variant/bcf2/BCF2UtilsUnitTest.java | 25 +-
.../variantcontext/filter/AllFailFilter.java} | 68 +-
.../variantcontext/filter/AllPassFilter.java} | 68 +-
.../variantcontext/filter/CompoundFilterTest.java | 78 ++
.../filter/FilteringIteratorTest.java | 88 ++
.../filter/GenotypeQualityFilterTest.java | 105 ++
.../filter/HeterozygosityFilterTest.java | 128 +++
.../filter/PassingVariantFilterTest.java | 46 +
.../variantcontext/filter/SnpFilterTest.java | 54 +
.../VariantContextWriterBuilderUnitTest.java | 10 +
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 34 +-
.../cram/CRAMException/testContigNotInRef.cram | Bin 0 -> 3433 bytes
.../cram/CRAMException/testContigNotInRef.cram.bai | Bin 0 -> 96 bytes
.../cram/CRAMException/testContigNotInRef.dict | 2 +
.../cram/CRAMException/testContigNotInRef.fa | 2 +
.../cram/CRAMException/testContigNotInRef.fa.fai | 1 +
.../cram/CRAMException/testContigNotInRef.fasta | 2 +
testdata/htsjdk/samtools/cram_tlen.fasta | 41 +
testdata/htsjdk/samtools/cram_tlen.fasta.fai | 8 +
.../htsjdk/samtools/cram_tlen_reads.sorted.sam | 19 +
testdata/htsjdk/samtools/cram_with_bai_index.cram | Bin 0 -> 4213 bytes
.../htsjdk/samtools/cram_with_bai_index.cram.bai | Bin 0 -> 336 bytes
testdata/htsjdk/samtools/cram_with_crai_index.cram | Bin 0 -> 4213 bytes
.../htsjdk/samtools/cram_with_crai_index.cram.crai | Bin 0 -> 77 bytes
testdata/htsjdk/samtools/hg19mini.fasta | 804 +++++++++++++++
testdata/htsjdk/samtools/hg19mini.fasta.fai | 4 +
.../htsjdk/samtools/metrics/metricsOne.metrics | 13 +
.../htsjdk/samtools/metrics/metricsOneCopy.metrics | 13 +
.../metrics/metricsOneModifiedHistogram.metrics | 14 +
.../metrics/metricsOneModifiedMetrics.metrics | 13 +
testdata/htsjdk/samtools/sra/test_archive.sra | Bin 0 -> 1099831 bytes
165 files changed, 11274 insertions(+), 1401 deletions(-)
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