[med-svn] [htsjdk] 01/03: Merge branch 'master' into debian/jessie-backports
Andreas Tille
tille at debian.org
Tue Apr 26 18:57:46 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian/jessie-backports
in repository htsjdk.
commit 40634f7ac0b84d3ec81599f07dbbf1bcc004d24d
Merge: 836c904 a515a1f
Author: Andreas Tille <tille at debian.org>
Date: Sun Apr 10 08:10:32 2016 +0200
Merge branch 'master' into debian/jessie-backports
.github/ISSUE_TEMPLATE.md | 21 +
.github/PULL_REQUEST_TEMPLATE.md | 11 +
.idea/modules/htsjdk.iml | 3 +-
.travis.yml | 7 +-
README.md | 4 +
build.sbt | 8 +-
build.xml | 69 +-
debian/changelog | 27 +-
debian/control | 14 +-
.../01-for-upstream-fix-version-in-manifest | 16 -
debian/patches/10-build.xml | 28 +-
debian/patches/11-snappy-java-compatibility.patch | 2 +-
debian/patches/12-use_libjbzip2-java | 4 +-
debian/patches/13-skip_network_tests | 633 +++++++++++
debian/patches/series | 2 +-
debian/rules | 10 +-
debian/watch | 2 +-
htsjdk.iml | 9 +
src/java/htsjdk/samtools/AbstractBAMFileIndex.java | 27 +-
src/java/htsjdk/samtools/BAMFileReader.java | 2 +-
.../{SAMFileSpan.java => BAMFileSpan.java} | 59 +-
src/java/htsjdk/samtools/BAMFileWriter.java | 2 +-
src/java/htsjdk/samtools/BAMIndexMetaData.java | 4 +-
src/java/htsjdk/samtools/BAMRecord.java | 7 +-
src/java/htsjdk/samtools/BAMRecordCodec.java | 6 +-
src/java/htsjdk/samtools/BamIndexValidator.java | 88 +-
src/java/htsjdk/samtools/BinaryTagCodec.java | 11 +-
...eWriter.java => CRAMContainerStreamWriter.java} | 333 +++---
src/java/htsjdk/samtools/CRAMFileReader.java | 210 +++-
src/java/htsjdk/samtools/CRAMFileWriter.java | 412 ++------
src/java/htsjdk/samtools/CRAMIndexer.java | 166 ++-
src/java/htsjdk/samtools/CRAMIterator.java | 56 +-
.../samtools/ChainedDownsamplingIterator.java | 90 ++
src/java/htsjdk/samtools/Cigar.java | 85 +-
src/java/htsjdk/samtools/CigarElement.java | 5 +
src/java/htsjdk/samtools/CigarOperator.java | 25 +
.../ConstantMemoryDownsamplingIterator.java | 88 ++
.../htsjdk/samtools/DefaultSAMRecordFactory.java | 6 +-
src/java/htsjdk/samtools/Defaults.java | 4 +-
.../htsjdk/samtools/DiskBasedBAMFileIndex.java | 8 +-
src/java/htsjdk/samtools/DownsamplingIterator.java | 164 ++-
.../samtools/DownsamplingIteratorFactory.java | 118 +++
.../htsjdk/samtools/DuplicateScoringStrategy.java | 39 +-
src/java/htsjdk/samtools/DuplicateSet.java | 70 +-
src/java/htsjdk/samtools/DuplicateSetIterator.java | 16 +-
.../samtools/HighAccuracyDownsamplingIterator.java | 196 ++++
.../htsjdk/samtools/MergingSamRecordIterator.java | 16 +-
.../SAMBinaryTagAndUnsignedArrayValue.java | 14 +-
src/java/htsjdk/samtools/SAMBinaryTagAndValue.java | 43 +-
src/java/htsjdk/samtools/SAMFileSpan.java | 244 -----
src/java/htsjdk/samtools/SAMFileWriterFactory.java | 200 +++-
src/java/htsjdk/samtools/SAMFileWriterImpl.java | 20 +-
.../htsjdk/samtools/SAMHeaderRecordComparator.java | 4 +-
src/java/htsjdk/samtools/SAMLineParser.java | 4 +-
src/java/htsjdk/samtools/SAMRecord.java | 769 +++++++++++---
.../samtools/SAMRecordCoordinateComparator.java | 12 +-
.../samtools/SAMRecordDuplicateComparator.java | 51 +-
.../samtools/SAMRecordQueryHashComparator.java | 72 ++
.../samtools/SAMRecordQueryNameComparator.java | 5 +-
src/java/htsjdk/samtools/SAMTag.java | 3 +
src/java/htsjdk/samtools/SAMTextHeaderCodec.java | 2 +-
src/java/htsjdk/samtools/SAMUtils.java | 189 +++-
src/java/htsjdk/samtools/SAMValidationError.java | 3 +-
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/SamFileHeaderMerger.java | 2 +-
src/java/htsjdk/samtools/SamFileValidator.java | 45 +-
src/java/htsjdk/samtools/SamFiles.java | 55 +-
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 | 72 +-
src/java/htsjdk/samtools/SamStreams.java | 1 +
src/java/htsjdk/samtools/TextTagCodec.java | 31 +-
.../htsjdk/samtools/TextualBAMIndexWriter.java | 2 +-
src/java/htsjdk/samtools/cram/CRAIEntry.java | 148 +++
src/java/htsjdk/samtools/cram/CRAIIndex.java | 164 +++
src/java/htsjdk/samtools/cram/CRAMException.java | 22 +
.../cram/build/CompressionHeaderFactory.java | 1118 ++++++++------------
.../samtools/cram/build/ContainerFactory.java | 29 +-
.../samtools/cram/build/ContainerParser.java | 88 +-
src/java/htsjdk/samtools/cram/build/CramIO.java | 34 +-
.../htsjdk/samtools/cram/build/CramNormalizer.java | 3 +
.../samtools/cram/build/Sam2CramRecordFactory.java | 15 +-
.../htsjdk/samtools/cram/common/CramVersions.java | 6 +-
.../codec/CanonicalHuffmanIntegerCodec.java | 8 +-
.../huffman/codec/HuffmanParamsCalculator.java | 137 +++
.../cram/encoding/reader/CramRecordReader.java | 22 +-
.../cram/encoding/reader/DataReaderFactory.java | 24 +-
.../cram/encoding/reader/RefSeqIdReader.java | 242 +++++
.../encoding/readfeatures/BaseQualityScore.java | 6 +-
.../cram/encoding/readfeatures/InsertBase.java | 6 +-
.../cram/encoding/readfeatures/ReadBase.java | 11 +-
.../cram/encoding/readfeatures/Substitution.java | 7 +-
.../cram/lossy/QualityScorePreservation.java | 2 +-
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 46 +-
.../samtools/cram/structure/AlignmentSpan.java | 92 ++
.../htsjdk/samtools/cram/structure/Container.java | 12 +-
.../cram/structure/CramCompressionRecord.java | 16 +-
.../htsjdk/samtools/cram/structure/ReadTag.java | 30 +-
src/java/htsjdk/samtools/cram/structure/Slice.java | 29 +-
.../cram/structure/SubstitutionMatrix.java | 4 +-
.../htsjdk/samtools/fastq/BasicFastqWriter.java | 6 +-
src/java/htsjdk/samtools/fastq/FastqReader.java | 1 +
src/java/htsjdk/samtools/fastq/FastqRecord.java | 20 +-
.../samtools/filter/AbstractJavascriptFilter.java | 159 +++
.../htsjdk/samtools/filter/FilteringIterator.java | 2 +-
.../htsjdk/samtools/filter/IntervalFilter.java | 2 +-
.../samtools/filter/JavascriptSamRecordFilter.java | 101 ++
.../samtools/filter/OverclippedReadFilter.java | 76 ++
src/java/htsjdk/samtools/metrics/MetricBase.java | 4 +-
src/java/htsjdk/samtools/metrics/MetricsFile.java | 42 +-
.../reference/AbstractFastaSequenceFile.java | 76 +-
.../samtools/reference/FastaSequenceFile.java | 18 +-
.../samtools/reference/FastaSequenceIndex.java | 21 +-
.../reference/IndexedFastaSequenceFile.java | 98 +-
.../reference/ReferenceSequenceFileFactory.java | 45 +-
.../seekablestream/SeekableMemoryStream.java | 64 ++
src/java/htsjdk/samtools/sra/ReferenceCache.java | 79 ++
src/java/htsjdk/samtools/sra/SRAAccession.java | 136 +++
.../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 | 10 +-
src/java/htsjdk/samtools/util/BinaryCodec.java | 18 +-
.../htsjdk/samtools/util/BufferedLineReader.java | 2 +-
src/java/htsjdk/samtools/util/CigarUtil.java | 4 +-
src/java/htsjdk/samtools/util/CollectionUtil.java | 59 +-
src/java/htsjdk/samtools/util/ComparableTuple.java | 28 +
src/java/htsjdk/samtools/util/DateParser.java | 30 +-
src/java/htsjdk/samtools/util/DiskBackedQueue.java | 14 +-
src/java/htsjdk/samtools/util/FormatUtil.java | 2 +-
src/java/htsjdk/samtools/util/Histogram.java | 20 +-
src/java/htsjdk/samtools/util/IOUtil.java | 66 +-
src/java/htsjdk/samtools/util/IntervalList.java | 9 +-
src/java/htsjdk/samtools/util/LocusComparator.java | 4 +-
src/java/htsjdk/samtools/util/Log.java | 12 +-
src/java/htsjdk/samtools/util/Murmur3.java | 119 +++
src/java/htsjdk/samtools/util/ProcessExecutor.java | 2 +-
src/java/htsjdk/samtools/util/ProgressLogger.java | 2 +-
...Comparator.java => RuntimeScriptException.java} | 24 +-
.../htsjdk/samtools/util/SamLocusIterator.java | 38 +-
.../samtools/util/SamRecordTrackingBuffer.java | 6 +-
src/java/htsjdk/samtools/util/SequenceUtil.java | 214 +++-
.../htsjdk/samtools/util/SortingCollection.java | 4 +-
.../samtools/util/SortingLongCollection.java | 4 +-
src/java/htsjdk/samtools/util/StringUtil.java | 16 +-
src/java/htsjdk/samtools/util/TrimmingUtil.java | 67 ++
src/java/htsjdk/samtools/util/Tuple.java | 26 +
src/java/htsjdk/tribble/bed/BEDCodec.java | 4 +-
.../index/interval/IntervalIndexCreator.java | 8 +-
.../tribble/index/interval/IntervalTree.java | 8 +-
.../tribble/index/interval/IntervalTreeIndex.java | 2 +-
.../tribble/index/linear/LinearIndexCreator.java | 4 +-
src/java/htsjdk/tribble/readers/TabixReader.java | 4 +-
src/java/htsjdk/variant/bcf2/BCF2Codec.java | 2 +-
src/java/htsjdk/variant/bcf2/BCF2Utils.java | 4 +-
.../htsjdk/variant/variantcontext/CommonInfo.java | 4 +-
.../htsjdk/variant/variantcontext/Genotype.java | 8 +-
.../variantcontext/GenotypeLikelihoods.java | 161 ++-
.../variant/variantcontext/VariantContext.java | 47 +-
.../variantcontext/VariantContextBuilder.java | 14 +-
.../variantcontext/VariantContextComparator.java | 8 +-
.../variantcontext/VariantContextUtils.java | 62 +-
.../variantcontext/filter/CompoundFilter.java | 74 ++
.../variantcontext/filter/FilteringIterator.java | 127 +++
.../filter/GenotypeQualityFilter.java | 79 ++
.../filter/HeterozygosityFilter.java | 84 ++
.../filter/JavascriptVariantFilter.java | 97 ++
.../filter/PassingVariantFilter.java} | 23 +-
.../variantcontext/filter/SnpFilter.java} | 23 +-
.../filter/VariantContextFilter.java} | 26 +-
.../variant/variantcontext/writer/BCF2Encoder.java | 2 +-
.../variantcontext/writer/BCF2FieldEncoder.java | 35 +-
.../writer/SortingVariantContextWriterBase.java | 5 +-
.../writer/VariantContextWriterBuilder.java | 25 +-
src/java/htsjdk/variant/vcf/AbstractVCFCodec.java | 8 +-
src/java/htsjdk/variant/vcf/VCF3Codec.java | 2 +-
src/java/htsjdk/variant/vcf/VCFCodec.java | 2 +-
src/java/htsjdk/variant/vcf/VCFEncoder.java | 34 +-
src/java/htsjdk/variant/vcf/VCFHeaderLine.java | 20 +-
src/java/htsjdk/variant/vcf/VCFRecordCodec.java | 18 +-
src/java/htsjdk/variant/vcf/VCFUtils.java | 2 +-
.../java/htsjdk/samtools/BAMFileWriterTest.java | 135 ++-
.../java/htsjdk/samtools/CRAMBAIIndexerTest.java | 87 ++
.../java/htsjdk/samtools/CRAMComplianceTest.java | 11 +-
.../samtools/CRAMContainerStreamWriterTest.java | 184 ++++
.../java/htsjdk/samtools/CRAMEdgeCasesTest.java | 33 +-
.../java/htsjdk/samtools/CRAMFileIndexTest.java | 104 +-
.../java/htsjdk/samtools/CRAMFileReaderTest.java | 163 +++
.../samtools/CRAMFileWriterWithIndexTest.java | 9 +-
src/tests/java/htsjdk/samtools/CigarTest.java | 105 +-
.../java/htsjdk/samtools/CramFileWriterTest.java | 170 ++-
.../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 | 957 ++++++++++++++++-
.../java/htsjdk/samtools/SAMTextWriterTest.java | 12 +
src/tests/java/htsjdk/samtools/SAMUtilsTest.java | 131 +++
src/tests/java/htsjdk/samtools/SamFilesTest.java | 81 ++
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/ValidateSamFileTest.java | 69 +-
.../java/htsjdk/samtools/cram/CRAIEntryTest.java | 145 +++
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 133 +++
.../samtools/cram/LosslessRoundTripTest.java | 68 ++
.../cram/build/CompressionHeaderFactoryTest.java | 208 ++++
.../samtools/cram/build/ContainerFactoryTest.java | 134 +++
.../samtools/cram/build/ContainerParserTest.java | 185 ++++
.../htsjdk/samtools/cram/build/CramIOTest.java | 82 ++
.../cram/encoding/huffman/codec/HuffmanTest.java | 18 +-
.../cram/structure/CramCompressionRecordTest.java | 68 ++
.../samtools/cram/structure/ReadTagTest.java | 21 +-
.../htsjdk/samtools/cram/structure/SliceTests.java | 36 +
.../htsjdk/samtools/fastq/FastqWriterTest.java | 73 ++
.../filter/JavascriptSamRecordFilterTest.java | 74 ++
.../samtools/filter/OverclippedReadFilterTest.java | 83 ++
.../htsjdk/samtools/metrics/MetricsFileTest.java | 21 +
.../samtools/reference/FastaSequenceIndexTest.java | 8 +-
.../reference/IndexedFastaSequenceFileTest.java | 10 +-
.../java/htsjdk/samtools/sra/AbstractSRATest.java | 57 +
.../java/htsjdk/samtools/sra/SRAAccessionTest.java | 29 +
.../java/htsjdk/samtools/sra/SRAIndexTest.java | 134 +++
.../htsjdk/samtools/sra/SRALazyRecordTest.java | 51 +
.../java/htsjdk/samtools/sra/SRAQueryTest.java | 73 ++
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 23 +
src/tests/java/htsjdk/samtools/sra/SRATest.java | 431 ++++++++
.../java/htsjdk/samtools/util/CodeUtilTest.java | 2 +-
.../htsjdk/samtools/util/ComparableTupleTest.java | 61 ++
.../htsjdk/samtools/util/DiskBackedQueueTest.java | 30 +-
src/tests/java/htsjdk/samtools/util/IupacTest.java | 2 +-
.../htsjdk/samtools/util/SequenceUtilTest.java | 256 ++++-
.../samtools/util/SortingCollectionTest.java | 39 +-
.../htsjdk/samtools/util/TrimmingUtilTest.java | 70 ++
src/tests/java/htsjdk/samtools/util/TupleTest.java | 62 ++
.../htsjdk/tribble/util/ftp/FTPClientTest.java | 77 +-
.../htsjdk/variant/bcf2/BCF2UtilsUnitTest.java | 25 +-
.../GenotypeLikelihoodsUnitTest.java | 161 ++-
.../variant/variantcontext/GenotypeUnitTest.java | 2 +
.../variantcontext/filter/AllFailFilter.java} | 20 +-
.../variantcontext/filter/AllPassFilter.java} | 20 +-
.../variantcontext/filter/CompoundFilterTest.java | 78 ++
.../filter/FilteringIteratorTest.java | 88 ++
.../filter/GenotypeQualityFilterTest.java | 105 ++
.../filter/HeterozygosityFilterTest.java | 128 +++
.../filter/JavascriptVariantFilterTest.java | 72 ++
.../filter/PassingVariantFilterTest.java | 46 +
.../variantcontext/filter/SnpFilterTest.java | 54 +
.../VariantContextWriterBuilderUnitTest.java | 10 +
.../htsjdk/variant/vcf/VCFHeaderLineUnitTest.java | 43 +
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 135 ++-
.../BAMFileIndexTest/symlink_with_index.bam | 1 +
.../BAMFileIndexTest/symlink_with_index.bam.bai | 1 +
.../symlink_without_linked_index.bam | 1 +
.../ValidateSamFileTest/duplicated_reads.sam | 17 +
.../duplicated_reads_out_of_order.sam | 17 +
.../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_query_sorted.cram | Bin 0 -> 13266 bytes
testdata/htsjdk/samtools/cram_query_sorted.fasta | 40 +
.../htsjdk/samtools/cram_query_sorted.fasta.fai | 8 +
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/samFilter01.js | 2 +
testdata/htsjdk/samtools/samFilter02.js | 9 +
testdata/htsjdk/samtools/sra/test_archive.sra | Bin 0 -> 1099831 bytes
testdata/htsjdk/variant/variantFilter01.js | 2 +
testdata/htsjdk/variant/variantFilter02.js | 20 +
293 files changed, 17600 insertions(+), 3004 deletions(-)
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