[med-svn] [htsjdk] 02/06: Merge tag 'upstream/2.1.1+dfsg.1' into sid
Vincent Danjean
vdanjean at debian.org
Mon Mar 14 20:11:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
vdanjean pushed a commit to branch master
in repository htsjdk.
commit a8546ae771efe33a7803d6cba70a920089097629
Merge: 592b540 a6a2d54
Author: Vincent Danjean <Vincent.Danjean at ens-lyon.org>
Date: Mon Mar 14 16:46:22 2016 +0100
Merge tag 'upstream/2.1.1+dfsg.1' into sid
Upstream version 2.1.1+dfsg.1
.github/ISSUE_TEMPLATE.md | 21 +
.github/PULL_REQUEST_TEMPLATE.md | 11 +
.travis.yml | 2 +-
README.md | 2 +
build.sbt | 2 +-
build.xml | 62 +-
src/java/htsjdk/samtools/BAMFileReader.java | 2 +-
src/java/htsjdk/samtools/BAMFileWriter.java | 2 +-
src/java/htsjdk/samtools/BAMIndexMetaData.java | 4 +-
src/java/htsjdk/samtools/BamIndexValidator.java | 88 +-
...eWriter.java => CRAMContainerStreamWriter.java} | 364 ++++---
src/java/htsjdk/samtools/CRAMFileReader.java | 146 ++-
src/java/htsjdk/samtools/CRAMFileWriter.java | 427 +-------
src/java/htsjdk/samtools/CRAMIndexer.java | 130 ++-
src/java/htsjdk/samtools/CRAMIterator.java | 34 +-
src/java/htsjdk/samtools/Cigar.java | 85 +-
src/java/htsjdk/samtools/CigarElement.java | 5 +
src/java/htsjdk/samtools/CigarOperator.java | 25 +
src/java/htsjdk/samtools/Defaults.java | 4 +-
.../htsjdk/samtools/DiskBasedBAMFileIndex.java | 8 +-
src/java/htsjdk/samtools/DuplicateSetIterator.java | 16 +-
.../samtools/HighAccuracyDownsamplingIterator.java | 2 +-
.../htsjdk/samtools/MergingSamRecordIterator.java | 4 +-
src/java/htsjdk/samtools/SAMFileWriterFactory.java | 55 +-
src/java/htsjdk/samtools/SAMFileWriterImpl.java | 12 +-
.../htsjdk/samtools/SAMHeaderRecordComparator.java | 4 +-
src/java/htsjdk/samtools/SAMLineParser.java | 4 +-
src/java/htsjdk/samtools/SAMRecord.java | 243 +++--
.../samtools/SAMRecordCoordinateComparator.java | 6 +-
.../samtools/SAMRecordDuplicateComparator.java | 5 +-
.../samtools/SAMRecordQueryHashComparator.java | 8 +-
.../samtools/SAMRecordQueryNameComparator.java | 5 +-
src/java/htsjdk/samtools/SAMTextHeaderCodec.java | 2 +-
src/java/htsjdk/samtools/SAMUtils.java | 15 +-
src/java/htsjdk/samtools/SAMValidationError.java | 3 +-
src/java/htsjdk/samtools/SamFileHeaderMerger.java | 2 +-
src/java/htsjdk/samtools/SamFileValidator.java | 24 +-
src/java/htsjdk/samtools/SamFiles.java | 32 +-
src/java/htsjdk/samtools/SamReaderFactory.java | 29 +-
src/java/htsjdk/samtools/TextTagCodec.java | 12 +-
.../htsjdk/samtools/TextualBAMIndexWriter.java | 2 +-
src/java/htsjdk/samtools/cram/CRAIIndex.java | 2 +-
.../cram/build/CompressionHeaderFactory.java | 1118 ++++++++------------
.../samtools/cram/build/ContainerFactory.java | 29 +-
.../samtools/cram/build/ContainerParser.java | 81 +-
src/java/htsjdk/samtools/cram/build/CramIO.java | 24 +-
.../htsjdk/samtools/cram/build/CramNormalizer.java | 3 +
.../samtools/cram/build/Sam2CramRecordFactory.java | 2 -
.../htsjdk/samtools/cram/common/CramVersions.java | 6 +-
.../codec/CanonicalHuffmanIntegerCodec.java | 8 +-
.../huffman/codec/HuffmanParamsCalculator.java | 137 +++
.../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 | 37 +
.../samtools/cram/structure/AlignmentSpan.java | 92 ++
.../htsjdk/samtools/cram/structure/Container.java | 12 +-
.../cram/structure/CramCompressionRecord.java | 10 +-
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 +++
.../samtools/filter/JavascriptSamRecordFilter.java | 101 ++
src/java/htsjdk/samtools/metrics/MetricBase.java | 4 +-
src/java/htsjdk/samtools/metrics/MetricsFile.java | 10 +-
.../reference/AbstractFastaSequenceFile.java | 2 +-
.../reference/IndexedFastaSequenceFile.java | 2 +-
src/java/htsjdk/samtools/sra/SRAAccession.java | 36 +-
.../samtools/util/AbstractProgressLogger.java | 8 +-
src/java/htsjdk/samtools/util/BinaryCodec.java | 8 +-
.../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 | 2 +-
src/java/htsjdk/samtools/util/FormatUtil.java | 2 +-
src/java/htsjdk/samtools/util/IOUtil.java | 4 +-
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 | 6 +-
src/java/htsjdk/samtools/util/ProcessExecutor.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 | 157 ++-
.../htsjdk/samtools/util/SortingCollection.java | 4 +-
.../samtools/util/SortingLongCollection.java | 4 +-
src/java/htsjdk/samtools/util/StringUtil.java | 12 +-
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 | 39 +-
.../variantcontext/VariantContextBuilder.java | 14 +-
.../variantcontext/VariantContextComparator.java | 8 +-
.../variantcontext/VariantContextUtils.java | 62 +-
.../filter/JavascriptVariantFilter.java | 97 ++
.../variant/variantcontext/writer/BCF2Encoder.java | 2 +-
.../writer/SortingVariantContextWriterBase.java | 5 +-
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/VCFUtils.java | 2 +-
.../java/htsjdk/samtools/BAMFileWriterTest.java | 42 +-
.../java/htsjdk/samtools/CRAMBAIIndexerTest.java | 87 ++
.../java/htsjdk/samtools/CRAMComplianceTest.java | 4 +-
.../samtools/CRAMContainerStreamWriterTest.java | 184 ++++
.../java/htsjdk/samtools/CRAMFileIndexTest.java | 40 +-
.../java/htsjdk/samtools/CRAMFileReaderTest.java | 163 +++
.../samtools/CRAMFileWriterWithIndexTest.java | 6 +-
src/tests/java/htsjdk/samtools/CigarTest.java | 24 +
.../java/htsjdk/samtools/CramFileWriterTest.java | 48 +
.../java/htsjdk/samtools/SAMFileReaderTest.java | 2 +-
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 162 ++-
src/tests/java/htsjdk/samtools/SAMUtilsTest.java | 37 +-
src/tests/java/htsjdk/samtools/SamFilesTest.java | 21 +
.../java/htsjdk/samtools/ValidateSamFileTest.java | 69 +-
.../samtools/cram/LosslessRoundTripTest.java | 68 ++
.../cram/build/CompressionHeaderFactoryTest.java | 208 ++++
.../samtools/cram/build/ContainerFactoryTest.java | 134 +++
.../samtools/cram/build/ContainerParserTest.java | 185 ++++
.../cram/encoding/huffman/codec/HuffmanTest.java | 18 +-
.../htsjdk/samtools/cram/structure/SliceTests.java | 36 +
.../htsjdk/samtools/fastq/FastqWriterTest.java | 73 ++
.../filter/JavascriptSamRecordFilterTest.java | 74 ++
.../java/htsjdk/samtools/sra/AbstractSRATest.java | 57 +
.../java/htsjdk/samtools/sra/SRAAccessionTest.java | 29 +
.../java/htsjdk/samtools/sra/SRAIndexTest.java | 56 +-
.../htsjdk/samtools/sra/SRALazyRecordTest.java | 12 +-
.../java/htsjdk/samtools/sra/SRAQueryTest.java | 67 +-
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 10 +-
src/tests/java/htsjdk/samtools/sra/SRATest.java | 115 +-
.../htsjdk/samtools/util/ComparableTupleTest.java | 61 ++
src/tests/java/htsjdk/samtools/util/IupacTest.java | 2 +-
.../htsjdk/samtools/util/SequenceUtilTest.java | 236 ++++-
.../htsjdk/samtools/util/TrimmingUtilTest.java | 70 ++
src/tests/java/htsjdk/samtools/util/TupleTest.java | 62 ++
.../htsjdk/tribble/util/ftp/FTPClientTest.java | 77 +-
.../GenotypeLikelihoodsUnitTest.java | 161 ++-
.../variant/variantcontext/GenotypeUnitTest.java | 2 +
.../filter/JavascriptVariantFilterTest.java | 72 ++
.../htsjdk/variant/vcf/VCFHeaderLineUnitTest.java | 43 +
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 101 +-
.../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 +
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/samFilter01.js | 2 +
testdata/htsjdk/samtools/samFilter02.js | 9 +
testdata/htsjdk/variant/variantFilter01.js | 2 +
testdata/htsjdk/variant/variantFilter02.js | 20 +
174 files changed, 6000 insertions(+), 2200 deletions(-)
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