This is an automated email from the git hooks/post-receive script. vdanjean pushed a commit to branch debian/jessie-backports in repository htsjdk.
commit 40634f7ac0b84d3ec81599f07dbbf1bcc004d24d Merge: 836c904 a515a1f Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htsjdk.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
