[med-svn] [htsjdk] 02/10: Merge tag 'upstream/2.5.0'
Andreas Tille
tille at debian.org
Wed Jun 29 12:18:43 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository htsjdk.
commit 23d85cbdce4d42404374e479fa0b4aa8a921e86d
Merge: a456695 c9883b4
Author: Andreas Tille <tille at debian.org>
Date: Wed Jun 29 09:25:52 2016 +0200
Merge tag 'upstream/2.5.0'
Upstream version 2.5.0
.classpath | 10 -
.github/PULL_REQUEST_TEMPLATE.md | 2 +
.gitignore | 25 +-
.idea/.name | 1 -
.idea/compiler.xml | 23 -
.idea/copyright/profiles_settings.xml | 3 -
.idea/encodings.xml | 4 -
.idea/modules.xml | 9 -
.idea/modules/htsjdk-build.iml | 81 -
.idea/modules/htsjdk.iml | 44 -
.idea/sbt.xml | 22 -
.idea/scala_compiler.xml | 6 -
.idea/scopes/scope_settings.xml | 5 -
.idea/vcs.xml | 7 -
.project | 17 -
.travis.yml | 23 +-
README.md | 67 +-
build.gradle | 226 +
build.sbt | 154 -
build.xml | 281 +-
etc/test/junit-noframes.xsl | 581 ---
etc/test/testng.css | 26 -
gradle/wrapper/gradle-wrapper.jar | Bin 0 -> 53556 bytes
gradle/wrapper/gradle-wrapper.properties | 6 +
gradlew | 164 +
htsjdk.iml | 66 -
htsjdk.ipr | 352 --
project/plugins.sbt | 5 -
{src/scripts => scripts}/explain_sam_flags.py | 0
{src/scripts => scripts}/release_picard.sh | 0
src/c/inteldeflater/IntelDeflater.c | 392 --
src/c/inteldeflater/README | 7 -
src/c/inteldeflater/igzip_lib.h | 50 -
src/c/inteldeflater/internal_state_size.h | 32 -
src/c/inteldeflater/types.h | 46 -
src/java/htsjdk/samtools/BAMFileReader.java | 989 ----
src/java/htsjdk/samtools/BAMFileWriter.java | 193 -
src/java/htsjdk/samtools/CRAMFileReader.java | 625 ---
src/java/htsjdk/samtools/CRAMIterator.java | 306 --
src/java/htsjdk/samtools/Defaults.java | 186 -
src/java/htsjdk/samtools/SAMFileReader.java | 751 ---
src/java/htsjdk/samtools/SAMFileWriterFactory.java | 465 --
src/java/htsjdk/samtools/SAMFlag.java | 110 -
src/java/htsjdk/samtools/SAMLineParser.java | 469 --
src/java/htsjdk/samtools/SAMRecordSetBuilder.java | 577 ---
src/java/htsjdk/samtools/SAMTextWriter.java | 188 -
src/java/htsjdk/samtools/SRAFileReader.java | 306 --
src/java/htsjdk/samtools/SRAIterator.java | 248 -
src/java/htsjdk/samtools/SamFileValidator.java | 856 ----
src/java/htsjdk/samtools/SamFiles.java | 81 -
src/java/htsjdk/samtools/SamInputResource.java | 360 --
src/java/htsjdk/samtools/SamReaderFactory.java | 507 --
src/java/htsjdk/samtools/SamStreams.java | 99 -
src/java/htsjdk/samtools/cram/CRAIEntry.java | 177 -
src/java/htsjdk/samtools/cram/CRAIIndex.java | 161 -
.../htsjdk/samtools/cram/common/CramVersions.java | 11 -
.../samtools/cram/io/ExternalCompression.java | 151 -
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 274 --
.../samtools/cram/structure/ContainerHeaderIO.java | 88 -
.../htsjdk/samtools/example/PrintReadsExample.java | 104 -
.../htsjdk/samtools/fastq/FastqWriterFactory.java | 31 -
src/java/htsjdk/samtools/liftover/LiftOver.java | 292 --
src/java/htsjdk/samtools/metrics/MetricsFile.java | 592 ---
.../seekablestream/SeekableMemoryStream.java | 64 -
.../seekablestream/SeekableStreamFactory.java | 95 -
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 -
.../samtools/util/BlockCompressedOutputStream.java | 336 --
src/java/htsjdk/samtools/util/Histogram.java | 480 --
src/java/htsjdk/samtools/util/Objects.java | 12 -
src/java/htsjdk/samtools/util/OverlapDetector.java | 126 -
.../htsjdk/samtools/util/SamLocusIterator.java | 552 ---
.../htsjdk/samtools/util/SortingCollection.java | 532 ---
.../htsjdk/samtools/util/zip/DeflaterFactory.java | 78 -
.../htsjdk/samtools/util/zip/IntelDeflater.java | 567 ---
src/java/htsjdk/samtools/util/zip/ZStreamRef.java | 48 -
src/java/htsjdk/tribble/AsciiFeatureCodec.java | 97 -
src/java/htsjdk/tribble/TabixFeatureReader.java | 221 -
.../tribble/readers/AsynchronousLineReader.java | 98 -
.../htsjdk/tribble/readers/LineReaderUtil.java | 94 -
src/java/htsjdk/variant/bcf2/BCF2Codec.java | 494 --
.../variant/example/PrintVariantsExample.java | 105 -
.../variantcontext/VariantContextBuilder.java | 500 --
.../writer/VariantContextWriterBuilder.java | 525 --
.../writer/VariantContextWriterFactory.java | 282 --
.../variant/vcf/VCFHeaderLineTranslator.java | 157 -
.../java/htsjdk/samtools/AbstractBAMFileIndex.java | 0
.../htsjdk/samtools/AbstractSAMHeaderRecord.java | 0
.../java/htsjdk/samtools/AlignmentBlock.java | 0
.../java/htsjdk/samtools/AsyncSAMFileWriter.java | 0
.../java/htsjdk/samtools/BAMFileConstants.java | 0
src/main/java/htsjdk/samtools/BAMFileReader.java | 913 ++++
.../java/htsjdk/samtools/BAMFileSpan.java | 0
src/main/java/htsjdk/samtools/BAMFileWriter.java | 200 +
src/{ => main}/java/htsjdk/samtools/BAMIndex.java | 0
.../java/htsjdk/samtools/BAMIndexContent.java | 0
.../java/htsjdk/samtools/BAMIndexMetaData.java | 0
.../java/htsjdk/samtools/BAMIndexWriter.java | 0
.../java/htsjdk/samtools/BAMIndexer.java | 0
.../java/htsjdk/samtools/BAMIteratorFilter.java | 26 +
.../BAMQueryMultipleIntervalsIteratorFilter.java | 59 +
src/{ => main}/java/htsjdk/samtools/BAMRecord.java | 0
.../java/htsjdk/samtools/BAMRecordCodec.java | 0
.../java/htsjdk/samtools/BamFileIoUtils.java | 0
.../java/htsjdk/samtools/BamIndexValidator.java | 0
src/{ => main}/java/htsjdk/samtools/Bin.java | 0
src/{ => main}/java/htsjdk/samtools/BinList.java | 0
.../java/htsjdk/samtools/BinaryBAMIndexWriter.java | 0
.../java/htsjdk/samtools/BinaryCigarCodec.java | 0
.../java/htsjdk/samtools/BinaryTagCodec.java | 0
.../java/htsjdk/samtools/BinningIndexBuilder.java | 0
.../java/htsjdk/samtools/BinningIndexContent.java | 0
.../java/htsjdk/samtools/BrowseableBAMIndex.java | 0
.../java/htsjdk/samtools/CRAMBAIIndexer.java | 0
src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java | 135 +
.../htsjdk/samtools/CRAMContainerStreamWriter.java | 0
src/main/java/htsjdk/samtools/CRAMFileReader.java | 533 +++
.../java/htsjdk/samtools/CRAMFileWriter.java | 0
src/main/java/htsjdk/samtools/CRAMIterator.java | 306 ++
.../java/htsjdk/samtools/CachingBAMFileIndex.java | 0
.../samtools/ChainedDownsamplingIterator.java | 0
src/{ => main}/java/htsjdk/samtools/Chunk.java | 0
src/{ => main}/java/htsjdk/samtools/Cigar.java | 0
.../java/htsjdk/samtools/CigarElement.java | 0
.../java/htsjdk/samtools/CigarOperator.java | 0
.../samtools/ComparableSamRecordIterator.java | 0
.../ConstantMemoryDownsamplingIterator.java | 0
.../samtools/CoordinateSortedPairInfoMap.java | 0
.../java/htsjdk/samtools/CustomReaderFactory.java | 0
.../htsjdk/samtools/DefaultSAMRecordFactory.java | 0
src/main/java/htsjdk/samtools/Defaults.java | 174 +
.../htsjdk/samtools/DiskBasedBAMFileIndex.java | 0
.../java/htsjdk/samtools/DownsamplingIterator.java | 0
.../samtools/DownsamplingIteratorFactory.java | 0
.../htsjdk/samtools/DuplicateScoringStrategy.java | 0
.../java/htsjdk/samtools/DuplicateSet.java | 0
.../java/htsjdk/samtools/DuplicateSetIterator.java | 0
.../htsjdk/samtools/FileTruncatedException.java | 0
.../java/htsjdk/samtools/FixBAMFile.java | 0
.../java/htsjdk/samtools/GenomicIndexUtil.java | 0
.../samtools/HighAccuracyDownsamplingIterator.java | 0
.../java/htsjdk/samtools/LinearIndex.java | 0
.../htsjdk/samtools/MergingSamRecordIterator.java | 0
.../samtools/NotPrimarySkippingIterator.java | 0
.../java/htsjdk/samtools/QueryInterval.java | 0
.../java/htsjdk/samtools/ReservedTagConstants.java | 0
.../SAMBinaryTagAndUnsignedArrayValue.java | 0
.../java/htsjdk/samtools/SAMBinaryTagAndValue.java | 0
.../java/htsjdk/samtools/SAMException.java | 0
.../java/htsjdk/samtools/SAMFileHeader.java | 0
src/main/java/htsjdk/samtools/SAMFileReader.java | 751 +++
.../java/htsjdk/samtools/SAMFileSource.java | 0
.../java/htsjdk/samtools/SAMFileSpan.java | 0
.../htsjdk/samtools/SAMFileTruncatedReader.java | 0
.../java/htsjdk/samtools/SAMFileWriter.java | 0
.../java/htsjdk/samtools/SAMFileWriterFactory.java | 505 ++
.../java/htsjdk/samtools/SAMFileWriterImpl.java | 0
src/main/java/htsjdk/samtools/SAMFlag.java | 110 +
.../java/htsjdk/samtools/SAMFormatException.java | 0
.../htsjdk/samtools/SAMHeaderRecordComparator.java | 0
src/main/java/htsjdk/samtools/SAMLineParser.java | 487 ++
.../java/htsjdk/samtools/SAMProgramRecord.java | 0
.../java/htsjdk/samtools/SAMReadGroupRecord.java | 0
src/{ => main}/java/htsjdk/samtools/SAMRecord.java | 0
.../java/htsjdk/samtools/SAMRecordComparator.java | 0
.../samtools/SAMRecordCoordinateComparator.java | 0
.../samtools/SAMRecordDuplicateComparator.java | 0
.../java/htsjdk/samtools/SAMRecordFactory.java | 0
.../java/htsjdk/samtools/SAMRecordIterator.java | 0
.../samtools/SAMRecordQueryHashComparator.java | 0
.../samtools/SAMRecordQueryNameComparator.java | 0
.../java/htsjdk/samtools/SAMRecordSetBuilder.java | 576 +++
.../java/htsjdk/samtools/SAMRecordUtil.java | 0
.../htsjdk/samtools/SAMSequenceDictionary.java | 0
.../java/htsjdk/samtools/SAMSequenceRecord.java | 0
.../java/htsjdk/samtools/SAMSortOrderChecker.java | 0
src/{ => main}/java/htsjdk/samtools/SAMTag.java | 0
.../java/htsjdk/samtools/SAMTagUtil.java | 0
.../java/htsjdk/samtools/SAMTestUtil.java | 0
.../java/htsjdk/samtools/SAMTextHeaderCodec.java | 0
.../java/htsjdk/samtools/SAMTextReader.java | 0
src/main/java/htsjdk/samtools/SAMTextWriter.java | 221 +
src/{ => main}/java/htsjdk/samtools/SAMTools.java | 0
src/{ => main}/java/htsjdk/samtools/SAMUtils.java | 0
.../java/htsjdk/samtools/SAMValidationError.java | 0
src/{ => main}/java/htsjdk/samtools/SQTagUtil.java | 0
src/main/java/htsjdk/samtools/SRAFileReader.java | 308 ++
src/{ => main}/java/htsjdk/samtools/SRAIndex.java | 0
src/main/java/htsjdk/samtools/SRAIterator.java | 256 +
.../java/htsjdk/samtools/SamFileHeaderMerger.java | 0
.../java/htsjdk/samtools/SamFileValidator.java | 856 ++++
src/main/java/htsjdk/samtools/SamFiles.java | 98 +
src/main/java/htsjdk/samtools/SamFlagField.java | 203 +
.../java/htsjdk/samtools/SamIndexes.java | 0
.../java/htsjdk/samtools/SamInputResource.java | 473 ++
.../java/htsjdk/samtools/SamPairUtil.java | 0
src/{ => main}/java/htsjdk/samtools/SamReader.java | 0
.../java/htsjdk/samtools/SamReaderFactory.java | 528 +++
src/main/java/htsjdk/samtools/SamStreams.java | 164 +
.../SecondaryOrSupplementarySkippingIterator.java | 0
.../StreamInflatingIndexingOutputStream.java | 0
.../samtools/TagValueAndUnsignedArrayFlag.java | 0
.../java/htsjdk/samtools/TextCigarCodec.java | 0
.../java/htsjdk/samtools/TextTagCodec.java | 0
.../htsjdk/samtools/TextualBAMIndexWriter.java | 0
.../java/htsjdk/samtools/ValidationStringency.java | 0
.../java/htsjdk/samtools/apps/TimeChannel.java | 0
.../htsjdk/samtools/apps/TimeRandomAccessFile.java | 0
src/main/java/htsjdk/samtools/cram/CRAIEntry.java | 195 +
src/main/java/htsjdk/samtools/cram/CRAIIndex.java | 267 ++
.../java/htsjdk/samtools/cram/CRAMException.java | 0
.../cram/build/CompressionHeaderFactory.java | 0
.../samtools/cram/build/ContainerFactory.java | 0
.../samtools/cram/build/ContainerParser.java | 0
.../samtools/cram/build/Cram2SamRecordFactory.java | 0
.../samtools/cram/build/CramContainerIterator.java | 0
.../java/htsjdk/samtools/cram/build/CramIO.java | 0
.../htsjdk/samtools/cram/build/CramNormalizer.java | 0
.../cram/build/CramSpanContainerIterator.java | 0
.../samtools/cram/build/Sam2CramRecordFactory.java | 0
.../java/htsjdk/samtools/cram/build/Utils.java | 0
.../samtools/cram/common/CramVersionPolicies.java | 0
.../htsjdk/samtools/cram/common/CramVersions.java | 11 +
.../htsjdk/samtools/cram/common/IntHashMap.java | 0
.../htsjdk/samtools/cram/common/MutableInt.java | 0
.../java/htsjdk/samtools/cram/common/Version.java | 0
.../samtools/cram/digest/AbstractSerialDigest.java | 0
.../samtools/cram/digest/ByteSumCombine.java | 0
.../java/htsjdk/samtools/cram/digest/Combine.java | 0
.../samtools/cram/digest/ContentDigests.java | 0
.../htsjdk/samtools/cram/digest/Crc32Hasher.java | 0
.../samtools/cram/digest/IntegerSumCombine.java | 0
.../samtools/cram/digest/MessageDigestHasher.java | 0
.../java/htsjdk/samtools/cram/digest/SERIES.java | 0
.../samtools/cram/encoding/AbstractBitCodec.java | 0
.../samtools/cram/encoding/BetaIntegerCodec.java | 0
.../cram/encoding/BetaIntegerEncoding.java | 0
.../htsjdk/samtools/cram/encoding/BitCodec.java | 0
.../cram/encoding/ByteArrayLenEncoding.java | 0
.../cram/encoding/ByteArrayStopEncoding.java | 0
.../htsjdk/samtools/cram/encoding/DataSeries.java | 0
.../samtools/cram/encoding/DataSeriesMap.java | 0
.../samtools/cram/encoding/DataSeriesType.java | 0
.../htsjdk/samtools/cram/encoding/Encoding.java | 0
.../samtools/cram/encoding/EncodingFactory.java | 0
.../cram/encoding/ExternalByteArrayCodec.java | 0
.../cram/encoding/ExternalByteArrayEncoding.java | 0
.../samtools/cram/encoding/ExternalByteCodec.java | 0
.../cram/encoding/ExternalByteEncoding.java | 0
.../samtools/cram/encoding/ExternalCompressor.java | 0
.../cram/encoding/ExternalIntegerCodec.java | 0
.../cram/encoding/ExternalIntegerEncoding.java | 0
.../samtools/cram/encoding/ExternalLongCodec.java | 0
.../cram/encoding/ExternalLongEncoding.java | 0
.../samtools/cram/encoding/GammaIntegerCodec.java | 0
.../cram/encoding/GammaIntegerEncoding.java | 0
.../samtools/cram/encoding/GolombIntegerCodec.java | 0
.../cram/encoding/GolombIntegerEncoding.java | 0
.../samtools/cram/encoding/GolombLongCodec.java | 0
.../samtools/cram/encoding/GolombLongEncoding.java | 0
.../cram/encoding/GolombRiceIntegerCodec.java | 0
.../cram/encoding/GolombRiceIntegerEncoding.java | 0
.../htsjdk/samtools/cram/encoding/NullCodec.java | 0
.../samtools/cram/encoding/NullEncoding.java | 0
.../cram/encoding/SubexponentialIntegerCodec.java | 0
.../encoding/SubexponentialIntegerEncoding.java | 0
.../cram/encoding/huffman/HuffmanCode.java | 0
.../cram/encoding/huffman/HuffmanLeaf.java | 0
.../cram/encoding/huffman/HuffmanNode.java | 0
.../cram/encoding/huffman/HuffmanTree.java | 0
.../huffman/codec/CanonicalHuffmanByteCodec.java | 0
.../codec/CanonicalHuffmanIntegerCodec.java | 0
.../encoding/huffman/codec/HuffmanBitCode.java | 0
.../huffman/codec/HuffmanByteEncoding.java | 0
.../encoding/huffman/codec/HuffmanByteHelper.java | 0
.../encoding/huffman/codec/HuffmanIntHelper.java | 0
.../huffman/codec/HuffmanIntegerEncoding.java | 0
.../huffman/codec/HuffmanParamsCalculator.java | 0
.../samtools/cram/encoding/rans/Constants.java | 0
.../htsjdk/samtools/cram/encoding/rans/D04.java | 0
.../htsjdk/samtools/cram/encoding/rans/D14.java | 0
.../samtools/cram/encoding/rans/Decoding.java | 0
.../htsjdk/samtools/cram/encoding/rans/E04.java | 0
.../htsjdk/samtools/cram/encoding/rans/E14.java | 0
.../samtools/cram/encoding/rans/Encoding.java | 0
.../samtools/cram/encoding/rans/Frequencies.java | 0
.../htsjdk/samtools/cram/encoding/rans/RANS.java | 0
.../htsjdk/samtools/cram/encoding/rans/Utils.java | 0
.../cram/encoding/reader/AbstractReader.java | 0
.../cram/encoding/reader/CramRecordReader.java | 0
.../samtools/cram/encoding/reader/DataReader.java | 0
.../cram/encoding/reader/DataReaderFactory.java | 0
.../cram/encoding/reader/RefSeqIdReader.java | 0
.../encoding/readfeatures/BaseQualityScore.java | 0
.../samtools/cram/encoding/readfeatures/Bases.java | 0
.../cram/encoding/readfeatures/Deletion.java | 0
.../cram/encoding/readfeatures/HardClip.java | 0
.../cram/encoding/readfeatures/InsertBase.java | 0
.../cram/encoding/readfeatures/Insertion.java | 0
.../cram/encoding/readfeatures/Padding.java | 0
.../cram/encoding/readfeatures/ReadBase.java | 0
.../cram/encoding/readfeatures/ReadFeature.java | 0
.../cram/encoding/readfeatures/RefSkip.java | 0
.../cram/encoding/readfeatures/Scores.java | 0
.../cram/encoding/readfeatures/SoftClip.java | 0
.../cram/encoding/readfeatures/Substitution.java | 0
.../samtools/cram/encoding/writer/DataWriter.java | 0
.../cram/encoding/writer/DataWriterFactory.java | 0
.../samtools/cram/encoding/writer/Writer.java | 0
.../htsjdk/samtools/cram/io/BitInputStream.java | 0
.../htsjdk/samtools/cram/io/BitOutputStream.java | 0
.../htsjdk/samtools/cram/io/CRC32InputStream.java | 0
.../htsjdk/samtools/cram/io/CRC32OutputStream.java | 0
.../samtools/cram/io/CountingInputStream.java | 0
.../java/htsjdk/samtools/cram/io/CramArray.java | 0
.../java/htsjdk/samtools/cram/io/CramInt.java | 0
.../samtools/cram/io/DefaultBitInputStream.java | 0
.../samtools/cram/io/DefaultBitOutputStream.java | 0
.../cram/io/ExposedByteArrayOutputStream.java | 0
.../samtools/cram/io/ExternalCompression.java | 152 +
.../java/htsjdk/samtools/cram/io/ITF8.java | 0
.../htsjdk/samtools/cram/io/InputStreamUtils.java | 0
.../java/htsjdk/samtools/cram/io/LTF8.java | 0
.../htsjdk/samtools/cram/lossy/BaseCategory.java | 0
.../samtools/cram/lossy/BaseCategoryType.java | 0
.../java/htsjdk/samtools/cram/lossy/Binning.java | 0
.../samtools/cram/lossy/PreservationPolicy.java | 0
.../cram/lossy/QualityScorePreservation.java | 0
.../samtools/cram/lossy/QualityScoreTreatment.java | 0
.../cram/lossy/QualityScoreTreatmentType.java | 0
.../htsjdk/samtools/cram/lossy/ReadCategory.java | 0
.../samtools/cram/lossy/ReadCategoryType.java | 0
.../samtools/cram/ref/CRAMReferenceSource.java | 0
.../htsjdk/samtools/cram/ref/EnaRefService.java | 0
.../cram/ref/InMemoryReferenceSequenceFile.java | 0
.../htsjdk/samtools/cram/ref/ReferenceRegion.java | 0
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 274 ++
.../htsjdk/samtools/cram/ref/ReferenceTracks.java | 0
.../samtools/cram/structure/AlignmentSpan.java | 0
.../java/htsjdk/samtools/cram/structure/Block.java | 0
.../cram/structure/BlockCompressionMethod.java | 0
.../samtools/cram/structure/BlockContentType.java | 0
.../samtools/cram/structure/CompressionHeader.java | 0
.../htsjdk/samtools/cram/structure/Container.java | 0
.../samtools/cram/structure/ContainerHeaderIO.java | 96 +
.../samtools/cram/structure/ContainerIO.java | 0
.../cram/structure/CramCompressionRecord.java | 0
.../htsjdk/samtools/cram/structure/CramHeader.java | 0
.../htsjdk/samtools/cram/structure/EncodingID.java | 0
.../samtools/cram/structure/EncodingKey.java | 0
.../samtools/cram/structure/EncodingParams.java | 0
.../htsjdk/samtools/cram/structure/ReadTag.java | 0
.../java/htsjdk/samtools/cram/structure/Slice.java | 0
.../htsjdk/samtools/cram/structure/SliceIO.java | 0
.../cram/structure/SubstitutionMatrix.java | 0
.../htsjdk/samtools/example/ExampleSamUsage.java | 0
.../htsjdk/samtools/example/PrintReadsExample.java | 98 +
.../htsjdk/samtools/fastq/AsyncFastqWriter.java | 0
.../htsjdk/samtools/fastq/BasicFastqWriter.java | 0
.../java/htsjdk/samtools/fastq/FastqConstants.java | 0
.../java/htsjdk/samtools/fastq/FastqReader.java | 0
.../java/htsjdk/samtools/fastq/FastqRecord.java | 0
.../java/htsjdk/samtools/fastq/FastqWriter.java | 0
.../htsjdk/samtools/fastq/FastqWriterFactory.java | 31 +
.../samtools/filter/AbstractJavascriptFilter.java | 0
.../htsjdk/samtools/filter/AggregateFilter.java | 0
.../java/htsjdk/samtools/filter/AlignedFilter.java | 0
.../samtools/filter/DuplicateReadFilter.java | 0
.../filter/FailsVendorReadQualityFilter.java | 0
.../htsjdk/samtools/filter/FilteringIterator.java | 0
.../samtools/filter/FilteringSamIterator.java | 0
.../htsjdk/samtools/filter/InsertSizeFilter.java | 0
.../htsjdk/samtools/filter/IntervalFilter.java | 0
.../samtools/filter/JavascriptSamRecordFilter.java | 0
.../samtools/filter/MappingQualityFilter.java | 0
.../samtools/filter/NotPrimaryAlignmentFilter.java | 0
.../samtools/filter/OverclippedReadFilter.java | 0
.../htsjdk/samtools/filter/ReadNameFilter.java | 0
.../htsjdk/samtools/filter/SamRecordFilter.java | 0
.../samtools/filter/SecondaryAlignmentFilter.java | 0
.../filter/SecondaryOrSupplementaryFilter.java | 0
.../htsjdk/samtools/filter/SolexaNoiseFilter.java | 0
.../java/htsjdk/samtools/filter/TagFilter.java | 0
.../samtools/filter/WholeReadClippedFilter.java | 0
.../java/htsjdk/samtools/liftover/Chain.java | 0
.../java/htsjdk/samtools/liftover/LiftOver.java | 319 ++
.../java/htsjdk/samtools/metrics/Header.java | 0
.../java/htsjdk/samtools/metrics/MetricBase.java | 0
.../java/htsjdk/samtools/metrics/MetricsFile.java | 594 +++
.../java/htsjdk/samtools/metrics/StringHeader.java | 0
.../htsjdk/samtools/metrics/VersionHeader.java | 0
.../reference/AbstractFastaSequenceFile.java | 0
.../samtools/reference/FastaSequenceFile.java | 0
.../samtools/reference/FastaSequenceIndex.java | 0
.../reference/IndexedFastaSequenceFile.java | 0
.../samtools/reference/ReferenceSequence.java | 0
.../samtools/reference/ReferenceSequenceFile.java | 0
.../reference/ReferenceSequenceFileFactory.java | 0
.../reference/ReferenceSequenceFileWalker.java | 0
.../seekablestream/ByteArraySeekableStream.java | 0
.../seekablestream/ISeekableStreamFactory.java | 0
.../seekablestream/SeekableBufferedStream.java | 0
.../samtools/seekablestream/SeekableFTPStream.java | 0
.../seekablestream/SeekableFTPStreamHelper.java | 0
.../seekablestream/SeekableFileStream.java | 0
.../seekablestream/SeekableHTTPStream.java | 0
.../seekablestream/SeekableMemoryStream.java | 64 +
.../seekablestream/SeekablePathStream.java | 121 +
.../samtools/seekablestream/SeekableStream.java | 0
.../seekablestream/SeekableStreamFactory.java | 97 +
.../samtools/seekablestream/UserPasswordInput.java | 0
.../java/htsjdk/samtools/sra/ReferenceCache.java | 46 +
.../java/htsjdk/samtools/sra/SRAAccession.java | 174 +
.../htsjdk/samtools/sra/SRAAlignmentIterator.java | 209 +
.../samtools/sra/SRAIndexedSequenceFile.java | 112 +
.../java/htsjdk/samtools/sra/SRALazyRecord.java | 0
.../samtools/sra/SRAUnalignmentIterator.java | 0
.../java/htsjdk/samtools/sra/SRAUtils.java | 0
.../htsjdk/samtools/util/AbstractAsyncWriter.java | 0
.../htsjdk/samtools/util/AbstractIterator.java | 0
.../samtools/util/AbstractProgressLogger.java | 0
.../java/htsjdk/samtools/util/AsciiWriter.java | 0
.../samtools/util/AsyncBufferedIterator.java | 0
.../java/htsjdk/samtools/util/BinaryCodec.java | 0
.../util/BlockCompressedFilePointerUtil.java | 0
.../samtools/util/BlockCompressedInputStream.java | 0
.../samtools/util/BlockCompressedOutputStream.java | 392 ++
.../util/BlockCompressedStreamConstants.java | 0
.../java/htsjdk/samtools/util/BlockGunzipper.java | 0
.../htsjdk/samtools/util/BufferedLineReader.java | 0
.../java/htsjdk/samtools/util/CigarUtil.java | 0
.../htsjdk/samtools/util/CloseableIterator.java | 0
.../java/htsjdk/samtools/util/CloserUtil.java | 0
.../java/htsjdk/samtools/util/CodeUtil.java | 0
.../java/htsjdk/samtools/util/CollectionUtil.java | 0
.../java/htsjdk/samtools/util/ComparableTuple.java | 0
.../java/htsjdk/samtools/util/CoordMath.java | 0
.../htsjdk/samtools/util/CoordSpanInputSteam.java | 0
.../java/htsjdk/samtools/util/DateParser.java | 0
.../htsjdk/samtools/util/DelegatingIterator.java | 0
.../java/htsjdk/samtools/util/DiskBackedQueue.java | 0
.../java/htsjdk/samtools/util/FastLineReader.java | 0
.../htsjdk/samtools/util/FastqQualityFormat.java | 0
.../samtools/util/FileAppendStreamLRUCache.java | 0
.../java/htsjdk/samtools/util/FormatUtil.java | 0
src/main/java/htsjdk/samtools/util/Histogram.java | 567 +++
.../java/htsjdk/samtools/util/HttpUtils.java | 0
.../java/htsjdk/samtools/util/IOUtil.java | 0
.../java/htsjdk/samtools/util/Interval.java | 0
.../java/htsjdk/samtools/util/IntervalList.java | 0
.../util/IntervalListReferenceSequenceMask.java | 0
.../java/htsjdk/samtools/util/IntervalTree.java | 0
.../java/htsjdk/samtools/util/IntervalTreeMap.java | 0
.../java/htsjdk/samtools/util/IntervalUtil.java | 0
.../java/htsjdk/samtools/util/Iso8601Date.java | 0
.../java/htsjdk/samtools/util/IterableAdapter.java | 0
.../htsjdk/samtools/util/IterableOnceIterator.java | 0
.../java/htsjdk/samtools/util/Iterables.java | 0
src/{ => main}/java/htsjdk/samtools/util/Lazy.java | 0
.../java/htsjdk/samtools/util/LineReader.java | 0
.../java/htsjdk/samtools/util/ListMap.java | 0
.../java/htsjdk/samtools/util/Locatable.java | 0
.../java/htsjdk/samtools/util/LocationAware.java | 0
.../java/htsjdk/samtools/util/Locus.java | 0
.../java/htsjdk/samtools/util/LocusComparator.java | 0
.../java/htsjdk/samtools/util/LocusImpl.java | 0
src/{ => main}/java/htsjdk/samtools/util/Log.java | 0
.../samtools/util/Md5CalculatingInputStream.java | 0
.../samtools/util/Md5CalculatingOutputStream.java | 0
.../java/htsjdk/samtools/util/MergingIterator.java | 0
.../java/htsjdk/samtools/util/Murmur3.java | 0
.../java/htsjdk/samtools/util/OverlapDetector.java | 193 +
.../java/htsjdk/samtools/util/PeekIterator.java | 0
.../htsjdk/samtools/util/PeekableIterator.java | 0
.../java/htsjdk/samtools/util/ProcessExecutor.java | 0
.../java/htsjdk/samtools/util/ProgressLogger.java | 0
.../samtools/util/ProgressLoggerInterface.java | 0
.../samtools/util/QualityEncodingDetector.java | 0
.../java/htsjdk/samtools/util/QualityUtil.java | 0
.../samtools/util/ReferenceSequenceMask.java | 0
.../htsjdk/samtools/util/RelativeIso8601Date.java | 0
.../htsjdk/samtools/util/ResourceLimitedMap.java | 0
.../samtools/util/ResourceLimitedMapFunctor.java | 0
.../htsjdk/samtools/util/RuntimeEOFException.java | 0
.../htsjdk/samtools/util/RuntimeIOException.java | 0
.../samtools/util/RuntimeScriptException.java | 0
.../htsjdk/samtools/util/SamLocusIterator.java | 679 +++
.../util/SamRecordIntervalIteratorFactory.java | 0
.../samtools/util/SamRecordTrackingBuffer.java | 0
.../htsjdk/samtools/util/SamRecordWithOrdinal.java | 0
.../java/htsjdk/samtools/util/SequenceUtil.java | 0
.../java/htsjdk/samtools/util/SnappyLoader.java | 0
.../samtools/util/SolexaQualityConverter.java | 0
.../htsjdk/samtools/util/SortingCollection.java | 514 ++
.../samtools/util/SortingLongCollection.java | 0
.../java/htsjdk/samtools/util/StopWatch.java | 0
.../htsjdk/samtools/util/StringLineReader.java | 0
.../java/htsjdk/samtools/util/StringUtil.java | 0
.../htsjdk/samtools/util/TempStreamFactory.java | 0
.../java/htsjdk/samtools/util/TestUtil.java | 0
.../java/htsjdk/samtools/util/TrimmingUtil.java | 0
.../java/htsjdk/samtools/util/Tuple.java | 0
.../util/WholeGenomeReferenceSequenceMask.java | 0
.../java/htsjdk/samtools/util/ftp/FTPClient.java | 0
.../java/htsjdk/samtools/util/ftp/FTPReply.java | 0
.../java/htsjdk/samtools/util/ftp/FTPStream.java | 0
.../java/htsjdk/samtools/util/ftp/FTPUtils.java | 0
.../htsjdk/samtools/util/zip/DeflaterFactory.java | 48 +
.../java/htsjdk/tribble/AbstractFeatureCodec.java | 0
.../java/htsjdk/tribble/AbstractFeatureReader.java | 0
.../java/htsjdk/tribble/AsciiFeatureCodec.java | 92 +
.../java/htsjdk/tribble/BinaryFeatureCodec.java | 0
.../htsjdk/tribble/CloseableTribbleIterator.java | 0
src/{ => main}/java/htsjdk/tribble/Feature.java | 0
.../java/htsjdk/tribble/FeatureCodec.java | 0
.../java/htsjdk/tribble/FeatureCodecHeader.java | 0
.../java/htsjdk/tribble/FeatureReader.java | 0
.../java/htsjdk/tribble/NameAwareCodec.java | 0
.../java/htsjdk/tribble/SimpleFeature.java | 0
.../java/htsjdk/tribble/TabixFeatureReader.java | 217 +
src/{ => main}/java/htsjdk/tribble/Tribble.java | 0
.../java/htsjdk/tribble/TribbleException.java | 0
.../tribble/TribbleIndexedFeatureReader.java | 0
.../java/htsjdk/tribble/annotation/Strand.java | 0
.../java/htsjdk/tribble/bed/BEDCodec.java | 0
.../java/htsjdk/tribble/bed/BEDFeature.java | 0
.../java/htsjdk/tribble/bed/FullBEDFeature.java | 0
.../java/htsjdk/tribble/bed/SimpleBEDFeature.java | 0
.../java/htsjdk/tribble/example/CountRecords.java | 0
.../htsjdk/tribble/example/ExampleBinaryCodec.java | 0
.../java/htsjdk/tribble/example/IndexToTable.java | 0
.../htsjdk/tribble/example/IndicesAreEqual.java | 0
.../tribble/example/ProfileIndexReading.java | 0
.../exception/CodecLineParsingException.java | 0
.../tribble/exception/UnsortedFileException.java | 0
.../htsjdk/tribble/gelitext/DiploidGenotype.java | 0
.../htsjdk/tribble/gelitext/GeliTextCodec.java | 0
.../htsjdk/tribble/gelitext/GeliTextFeature.java | 0
.../java/htsjdk/tribble/index/AbstractIndex.java | 0
.../java/htsjdk/tribble/index/Block.java | 0
.../java/htsjdk/tribble/index/ChrIndex.java | 0
.../htsjdk/tribble/index/DynamicIndexCreator.java | 0
.../java/htsjdk/tribble/index/Index.java | 0
.../java/htsjdk/tribble/index/IndexCreator.java | 0
.../java/htsjdk/tribble/index/IndexFactory.java | 0
.../java/htsjdk/tribble/index/MutableIndex.java | 0
.../htsjdk/tribble/index/TribbleIndexCreator.java | 0
.../htsjdk/tribble/index/interval/Interval.java | 0
.../index/interval/IntervalIndexCreator.java | 0
.../tribble/index/interval/IntervalTree.java | 0
.../tribble/index/interval/IntervalTreeIndex.java | 0
.../htsjdk/tribble/index/linear/LinearIndex.java | 0
.../tribble/index/linear/LinearIndexCreator.java | 0
.../htsjdk/tribble/index/tabix/TabixFormat.java | 0
.../htsjdk/tribble/index/tabix/TabixIndex.java | 0
.../tribble/index/tabix/TabixIndexCreator.java | 0
.../htsjdk/tribble/readers/AsciiLineReader.java | 0
.../tribble/readers/AsciiLineReaderIterator.java | 0
.../java/htsjdk/tribble/readers/LineIterator.java | 0
.../htsjdk/tribble/readers/LineIteratorImpl.java | 0
.../java/htsjdk/tribble/readers/LineReader.java | 0
.../htsjdk/tribble/readers/LineReaderUtil.java | 56 +
.../tribble/readers/LongLineBufferedReader.java | 0
.../java/htsjdk/tribble/readers/Positional.java | 0
.../tribble/readers/PositionalBufferedStream.java | 0
.../tribble/readers/SynchronousLineReader.java | 61 +
.../tribble/readers/TabixIteratorLineReader.java | 0
.../java/htsjdk/tribble/readers/TabixReader.java | 0
src/{ => main}/java/htsjdk/tribble/readme.txt | 0
.../java/htsjdk/tribble/util/FTPHelper.java | 0
.../java/htsjdk/tribble/util/HTTPHelper.java | 0
.../tribble/util/LittleEndianInputStream.java | 0
.../tribble/util/LittleEndianOutputStream.java | 0
.../java/htsjdk/tribble/util/MathUtils.java | 0
.../java/htsjdk/tribble/util/ParsingUtils.java | 0
.../java/htsjdk/tribble/util/RemoteURLHelper.java | 0
.../java/htsjdk/tribble/util/TabixUtils.java | 0
.../java/htsjdk/tribble/util/URLHelper.java | 0
.../java/htsjdk/tribble/util/ftp/.gitignore | 0
.../util/popgen/HardyWeinbergCalculation.java | 0
src/main/java/htsjdk/variant/bcf2/BCF2Codec.java | 491 ++
.../java/htsjdk/variant/bcf2/BCF2Decoder.java | 0
.../variant/bcf2/BCF2GenotypeFieldDecoders.java | 0
.../variant/bcf2/BCF2LazyGenotypesDecoder.java | 0
.../java/htsjdk/variant/bcf2/BCF2Type.java | 0
.../java/htsjdk/variant/bcf2/BCF2Utils.java | 0
.../java/htsjdk/variant/bcf2/BCFVersion.java | 0
.../variant/example/PrintVariantsExample.java | 103 +
.../java/htsjdk/variant/utils/GeneralUtils.java | 0
.../utils/SAMSequenceDictionaryExtractor.java | 0
.../java/htsjdk/variant/variantcontext/Allele.java | 0
.../htsjdk/variant/variantcontext/CommonInfo.java | 0
.../variant/variantcontext/FastGenotype.java | 0
.../htsjdk/variant/variantcontext/Genotype.java | 0
.../variant/variantcontext/GenotypeBuilder.java | 0
.../variantcontext/GenotypeJEXLContext.java | 0
.../variantcontext/GenotypeLikelihoods.java | 0
.../variant/variantcontext/GenotypeType.java | 0
.../variant/variantcontext/GenotypesContext.java | 0
.../htsjdk/variant/variantcontext/JEXLMap.java | 0
.../variantcontext/LazyGenotypesContext.java | 0
.../variant/variantcontext/VariantContext.java | 0
.../variantcontext/VariantContextBuilder.java | 498 ++
.../variantcontext/VariantContextComparator.java | 0
.../variantcontext/VariantContextUtils.java | 0
.../variant/variantcontext/VariantJEXLContext.java | 0
.../variantcontext/filter/CompoundFilter.java | 0
.../variantcontext/filter/FilteringIterator.java | 0
.../filter/FilteringVariantContextIterator.java | 0
.../filter/GenotypeQualityFilter.java | 0
.../filter/HeterozygosityFilter.java | 0
.../filter/JavascriptVariantFilter.java | 0
.../filter/PassingVariantFilter.java | 0
.../variant/variantcontext/filter/SnpFilter.java | 0
.../filter/VariantContextFilter.java | 0
.../writer/AsyncVariantContextWriter.java | 0
.../variant/variantcontext/writer/BCF2Encoder.java | 0
.../variantcontext/writer/BCF2FieldEncoder.java | 0
.../variantcontext/writer/BCF2FieldWriter.java | 0
.../writer/BCF2FieldWriterManager.java | 0
.../variant/variantcontext/writer/BCF2Writer.java | 0
.../writer/IndexingVariantContextWriter.java | 0
.../writer/IntGenotypeFieldAccessors.java | 0
.../variant/variantcontext/writer/Options.java | 0
.../writer/SortingVariantContextWriter.java | 0
.../writer/SortingVariantContextWriterBase.java | 0
.../variant/variantcontext/writer/VCFWriter.java | 0
.../writer/VariantContextWriter.java | 0
.../writer/VariantContextWriterBuilder.java | 537 +++
.../writer/VariantContextWriterFactory.java | 282 ++
.../java/htsjdk/variant/vcf/AbstractVCFCodec.java | 0
.../java/htsjdk/variant/vcf/VCF3Codec.java | 0
.../java/htsjdk/variant/vcf/VCFCodec.java | 0
.../htsjdk/variant/vcf/VCFCompoundHeaderLine.java | 0
.../java/htsjdk/variant/vcf/VCFConstants.java | 0
.../htsjdk/variant/vcf/VCFContigHeaderLine.java | 0
.../java/htsjdk/variant/vcf/VCFEncoder.java | 0
.../java/htsjdk/variant/vcf/VCFFileReader.java | 0
.../htsjdk/variant/vcf/VCFFilterHeaderLine.java | 0
.../htsjdk/variant/vcf/VCFFormatHeaderLine.java | 0
.../java/htsjdk/variant/vcf/VCFHeader.java | 0
.../java/htsjdk/variant/vcf/VCFHeaderLine.java | 0
.../htsjdk/variant/vcf/VCFHeaderLineCount.java | 0
.../variant/vcf/VCFHeaderLineTranslator.java | 183 +
.../java/htsjdk/variant/vcf/VCFHeaderLineType.java | 0
.../java/htsjdk/variant/vcf/VCFHeaderVersion.java | 0
.../java/htsjdk/variant/vcf/VCFIDHeaderLine.java | 0
.../java/htsjdk/variant/vcf/VCFInfoHeaderLine.java | 0
.../java/htsjdk/variant/vcf/VCFRecordCodec.java | 0
.../htsjdk/variant/vcf/VCFSimpleHeaderLine.java | 0
.../htsjdk/variant/vcf/VCFStandardHeaderLines.java | 0
.../java/htsjdk/variant/vcf/VCFUtils.java | 0
src/scripts/build_intel_deflater.sh | 78 -
.../htsjdk/cram/io/ExternalCompressionTest.java | 30 +
.../htsjdk/samtools/AbstractBAMFileIndexTest.java | 0
.../java/htsjdk/samtools/BAMCigarOverflowTest.java | 29 +
.../java/htsjdk/samtools/BAMFileIndexTest.java | 527 +++
.../java/htsjdk/samtools/BAMFileWriterTest.java | 0
.../java/htsjdk/samtools/BAMIndexWriterTest.java | 227 +
src/test/java/htsjdk/samtools/BAMIteratorTest.java | 71 +
...AMQueryMultipleIntervalsIteratorFilterTest.java | 146 +
.../java/htsjdk/samtools/BAMRemoteFileTest.java | 326 ++
.../java/htsjdk/samtools/BinTest.java | 0
.../java/htsjdk/samtools/CRAMBAIIndexerTest.java | 0
.../java/htsjdk/samtools/CRAMCRAIIndexerTest.java | 178 +
.../java/htsjdk/samtools/CRAMComplianceTest.java | 150 +
.../samtools/CRAMContainerStreamWriterTest.java | 184 +
.../java/htsjdk/samtools/CRAMEdgeCasesTest.java | 158 +
.../java/htsjdk/samtools/CRAMFileBAIIndexTest.java | 301 ++
.../htsjdk/samtools/CRAMFileCRAIIndexTest.java | 368 ++
.../java/htsjdk/samtools/CRAMFileReaderTest.java | 163 +
.../java/htsjdk/samtools/CRAMFileWriterTest.java | 282 ++
.../samtools/CRAMFileWriterWithIndexTest.java | 209 +
.../java/htsjdk/samtools/CRAMIndexQueryTest.java | 708 +++
.../java/htsjdk/samtools/ChunkTest.java | 0
.../java/htsjdk/samtools/CigarCodecTest.java | 0
.../java/htsjdk/samtools/CigarTest.java | 0
.../htsjdk/samtools/DownsamplingIteratorTests.java | 87 +
.../htsjdk/samtools/DuplicateSetIteratorTest.java | 0
.../java/htsjdk/samtools/GenomicIndexUtilTest.java | 0
...MergingSamRecordIteratorGroupCollisionTest.java | 0
.../samtools/MergingSamRecordIteratorTest.java | 0
.../htsjdk/samtools/ProgramRecordChainingTest.java | 0
.../samtools/SAMBinaryTagAndValueUnitTest.java | 0
.../java/htsjdk/samtools/SAMCloneTest.java | 0
.../java/htsjdk/samtools/SAMFileReaderTest.java | 170 +
.../htsjdk/samtools/SAMFileWriterFactoryTest.java | 307 ++
.../java/htsjdk/samtools/SAMFlagTest.java | 0
.../java/htsjdk/samtools/SAMIntegerTagTest.java | 329 ++
.../samtools/SAMRecordDuplicateComparatorTest.java | 0
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 963 ++++
.../htsjdk/samtools/SAMSequenceDictionaryTest.java | 0
.../java/htsjdk/samtools/SAMTextReaderTest.java | 0
.../java/htsjdk/samtools/SAMTextWriterTest.java | 130 +
.../java/htsjdk/samtools/SAMUtilsTest.java | 0
.../htsjdk/samtools/SamFileHeaderMergerTest.java | 265 ++
src/test/java/htsjdk/samtools/SamFilesTest.java | 91 +
.../java/htsjdk/samtools/SamFlagFieldTest.java | 150 +
.../samtools/SamHeaderRecordComparatorTest.java | 0
src/test/java/htsjdk/samtools/SamIndexesTest.java | 193 +
.../java/htsjdk/samtools/SamPairUtilTest.java | 0
.../java/htsjdk/samtools/SamReaderFactoryTest.java | 437 ++
.../java/htsjdk/samtools/SamReaderSortTest.java | 102 +
src/test/java/htsjdk/samtools/SamSpecIntTest.java | 97 +
src/test/java/htsjdk/samtools/SamStreamsTest.java | 124 +
.../SequenceNameTruncationAndValidationTest.java | 98 +
.../java/htsjdk/samtools/ValidateSamFileTest.java | 471 ++
.../java/htsjdk/samtools/apps/.gitignore | 0
.../java/htsjdk/samtools/cram/CRAIEntryTest.java | 0
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 220 +
.../samtools/cram/LosslessRoundTripTest.java | 0
.../java/htsjdk/samtools/cram/VersionTest.java | 106 +
.../cram/build/CompressionHeaderFactoryTest.java | 0
.../samtools/cram/build/ContainerFactoryTest.java | 0
.../samtools/cram/build/ContainerParserTest.java | 0
.../htsjdk/samtools/cram/build/CramIOTest.java | 0
.../cram/encoding/huffman/codec/HuffmanTest.java | 0
.../samtools/cram/encoding/rans/RansTest.java | 0
.../java/htsjdk/samtools/cram/io/ITF8Test.java | 0
.../java/htsjdk/samtools/cram/io/LTF8Test.java | 0
.../cram/lossy/QualityScorePreservationTest.java | 0
.../samtools/cram/ref/EnaRefServiceTest.java | 0
.../cram/structure/CramCompressionRecordTest.java | 0
.../samtools/cram/structure/ReadTagTest.java | 0
.../htsjdk/samtools/cram/structure/SliceTests.java | 0
.../cram/structure/SubstitutionMatrixTest.java | 0
.../java/htsjdk/samtools/fastq/.gitignore | 0
.../htsjdk/samtools/fastq/FastqRecordTest.java | 204 +
.../htsjdk/samtools/fastq/FastqWriterTest.java | 73 +
.../filter/FailsVendorReadQualityFilterTest.java | 0
.../samtools/filter/InsertSizeFilterTest.java | 0
.../filter/JavascriptSamRecordFilterTest.java | 74 +
.../samtools/filter/MappingQualityFilterTest.java | 0
.../samtools/filter/OverclippedReadFilterTest.java | 0
.../samtools/filter/SolexaNoiseFilterTest.java | 0
.../java/htsjdk/samtools/filter/TagFilterTest.java | 0
.../htsjdk/samtools/liftover/LiftOverTest.java | 468 ++
.../htsjdk/samtools/metrics/MetricBaseTest.java | 0
.../htsjdk/samtools/metrics/MetricsFileTest.java | 213 +
.../htsjdk/samtools/metrics/StringHeaderTest.java | 0
.../htsjdk/samtools/metrics/VersionHeaderTest.java | 0
.../reference/FakeReferenceSequenceFile.java | 0
.../samtools/reference/FastaSequenceFileTest.java | 85 +
.../samtools/reference/FastaSequenceIndexTest.java | 256 +
.../reference/InMemoryReferenceSequenceFile.java | 0
.../reference/IndexedFastaSequenceFileTest.java | 308 ++
.../ReferenceSequenceFileFactoryTests.java | 39 +
.../reference/ReferenceSequenceFileWalkerTest.java | 73 +
.../samtools/reference/ReferenceSequenceTests.java | 0
.../seekablestream/SeekableBufferedStreamTest.java | 162 +
.../seekablestream/SeekableFTPStreamTest.java | 0
.../seekablestream/SeekableFileStreamTest.java | 52 +
.../seekablestream/SeekableMemoryStreamTest.java | 93 +
.../seekablestream/SeekablePathStreamTest.java | 51 +
.../seekablestream/SeekableStreamFactoryTest.java | 44 +
.../java/htsjdk/samtools/sra/AbstractSRATest.java | 0
.../java/htsjdk/samtools/sra/SRAAccessionTest.java | 29 +
.../java/htsjdk/samtools/sra/SRAIndexTest.java | 0
.../htsjdk/samtools/sra/SRALazyRecordTest.java | 0
.../java/htsjdk/samtools/sra/SRAQueryTest.java | 0
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 95 +
src/test/java/htsjdk/samtools/sra/SRATest.java | 432 ++
.../samtools/util/AsyncBufferedIteratorTest.java | 0
.../java/htsjdk/samtools/util/BinaryCodecTest.java | 0
.../util/BlockCompressedFilePointerUtilTest.java | 0
.../util/BlockCompressedOutputStreamTest.java | 165 +
.../util/BlockCompressedTerminatorTest.java | 59 +
.../java/htsjdk/samtools/util/CigarUtilTest.java | 0
.../samtools/util/CloseableIteratorTest.java | 0
.../java/htsjdk/samtools/util/CodeUtilTest.java | 0
.../htsjdk/samtools/util/ComparableTupleTest.java | 0
.../samtools/util/CoordSpanInputSteamTest.java | 0
.../htsjdk/samtools/util/DiskBackedQueueTest.java | 0
.../java/htsjdk/samtools/util/HistogramTest.java | 366 ++
.../htsjdk/samtools/util/IntervalListTest.java | 520 ++
.../htsjdk/samtools/util/IntervalTreeMapTest.java | 0
.../htsjdk/samtools/util/IntervalTreeTest.java | 0
src/test/java/htsjdk/samtools/util/IoUtilTest.java | 190 +
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.../java/htsjdk/samtools/util/IupacTest.java | 0
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.../htsjdk/samtools/util/OverlapDetectorTest.java | 240 +
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.../htsjdk/samtools/util/SamLocusIteratorTest.java | 676 +++
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.../samtools/util/SolexaQualityConverterTest.java | 0
.../samtools/util/SortingCollectionTest.java | 0
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src/test/java/htsjdk/tribble/TestUtils.java | 28 +
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.../java/htsjdk/tribble/TribbleTest.java | 0
.../java/htsjdk/tribble/bed/BEDCodecTest.java | 0
.../java/htsjdk/tribble/gelitext/GeliTextTest.java | 0
.../htsjdk/tribble/index/IndexFactoryTest.java | 115 +
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.../tribble/index/interval/IntervalTreeTest.java | 0
.../tribble/index/linear/LinearIndexTest.java | 0
.../htsjdk/tribble/index/tabix/TabixIndexTest.java | 143 +
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.../readers/LongLineBufferedReaderTest.java | 0
.../readers/PositionalBufferedStreamTest.java | 0
.../java/htsjdk/tribble/readers/ReaderTest.java | 0
.../readers/SynchronousLineReaderUnitTest.java | 39 +
.../htsjdk/tribble/readers/TabixReaderTest.java | 0
.../java/htsjdk/tribble/source/.gitignore | 0
.../java/htsjdk/tribble/util/ParsingUtilsTest.java | 0
.../htsjdk/tribble/util/ftp/FTPClientTest.java | 0
.../java/htsjdk/tribble/util/ftp/FTPUtilsTest.java | 0
.../util/popgen/HardyWeinbergCalculationTest.java | 0
.../htsjdk/variant/PrintVariantsExampleTest.java | 65 +
src/test/java/htsjdk/variant/VariantBaseTest.java | 278 ++
.../variant/bcf2/BCF2EncoderDecoderUnitTest.java | 0
.../htsjdk/variant/bcf2/BCF2UtilsUnitTest.java | 0
.../utils/SAMSequenceDictionaryExtractorTest.java | 65 +
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.../GenotypeLikelihoodsUnitTest.java | 337 ++
.../variant/variantcontext/GenotypeUnitTest.java | 0
.../variantcontext/GenotypesContextUnitTest.java | 0
.../variantcontext/VariantContextBuilderTest.java | 0
.../variantcontext/VariantContextTestProvider.java | 1014 ++++
.../variantcontext/VariantContextUnitTest.java | 1450 ++++++
.../variantcontext/VariantJEXLContextUnitTest.java | 0
.../variantcontext/filter/AllFailFilter.java | 0
.../variantcontext/filter/AllPassFilter.java | 0
.../variantcontext/filter/CompoundFilterTest.java | 0
.../FilteringVariantContextIteratorTest.java | 88 +
.../filter/GenotypeQualityFilterTest.java | 0
.../filter/HeterozygosityFilterTest.java | 0
.../filter/JavascriptVariantFilterTest.java | 72 +
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.../variantcontext/filter/SnpFilterTest.java | 0
.../writer/TabixOnTheFlyIndexCreationTest.java | 66 +
.../variantcontext/writer/VCFWriterUnitTest.java | 280 ++
.../VariantContextWriterBuilderUnitTest.java | 399 ++
.../writer/VariantContextWritersUnitTest.java | 0
.../htsjdk/variant/vcf/AbstractVCFCodecTest.java | 53 +
.../htsjdk/variant/vcf/IndexFactoryUnitTest.java | 0
.../variant/vcf/VCFCompoundHeaderLineUnitTest.java | 0
.../java/htsjdk/variant/vcf/VCFEncoderTest.java | 0
.../vcf/VCFHeaderLineTranslatorUnitTest.java | 62 +
.../htsjdk/variant/vcf/VCFHeaderLineUnitTest.java | 0
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 561 +++
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.../samtools/cram/human_g1k_v37.20.21.1-100.fasta | 11 +
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.../cram/human_g1k_v37.20.21.10M-10M200k.fasta | 5002 ++++++++++++++++++++
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src/test/resources/htsjdk/samtools/hg19mini.dict | 5 +
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.../sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam | 0
.../sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam | 0
.../sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam | 0
.../sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam | 0
.../sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam | 0
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.../net/sf/picard/illumina/25T8B25T/sams/N.sam | 0
.../sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam | 0
.../sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam | 0
src/{tests => test}/resources/testng.xml | 0
.../test/resources}/tribble/tmp/.gitignore | 0
.../java/htsjdk/samtools/BAMCigarOverflowTest.java | 29 -
.../java/htsjdk/samtools/BAMFileIndexTest.java | 527 ---
.../java/htsjdk/samtools/BAMIndexWriterTest.java | 227 -
.../java/htsjdk/samtools/BAMIteratorTest.java | 71 -
.../java/htsjdk/samtools/BAMRemoteFileTest.java | 326 --
.../java/htsjdk/samtools/CRAMComplianceTest.java | 150 -
.../samtools/CRAMContainerStreamWriterTest.java | 184 -
.../java/htsjdk/samtools/CRAMEdgeCasesTest.java | 158 -
.../java/htsjdk/samtools/CRAMFileBAIIndexTest.java | 294 --
.../java/htsjdk/samtools/CRAMFileReaderTest.java | 163 -
.../java/htsjdk/samtools/CRAMFileWriterTest.java | 282 --
.../samtools/CRAMFileWriterWithIndexTest.java | 203 -
.../htsjdk/samtools/DownsamplingIteratorTests.java | 82 -
.../java/htsjdk/samtools/SAMFileReaderTest.java | 170 -
.../htsjdk/samtools/SAMFileWriterFactoryTest.java | 317 --
.../java/htsjdk/samtools/SAMIntegerTagTest.java | 329 --
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 963 ----
.../java/htsjdk/samtools/SAMTextWriterTest.java | 107 -
.../htsjdk/samtools/SamFileHeaderMergerTest.java | 265 --
src/tests/java/htsjdk/samtools/SamFilesTest.java | 81 -
src/tests/java/htsjdk/samtools/SamIndexesTest.java | 192 -
.../java/htsjdk/samtools/SamReaderFactoryTest.java | 293 --
.../java/htsjdk/samtools/SamReaderSortTest.java | 102 -
src/tests/java/htsjdk/samtools/SamSpecIntTest.java | 97 -
src/tests/java/htsjdk/samtools/SamStreamsTest.java | 60 -
.../SequenceNameTruncationAndValidationTest.java | 98 -
.../java/htsjdk/samtools/ValidateSamFileTest.java | 471 --
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 213 -
.../htsjdk/samtools/fastq/FastqWriterTest.java | 73 -
.../filter/JavascriptSamRecordFilterTest.java | 74 -
.../htsjdk/samtools/liftover/LiftOverTest.java | 458 --
.../htsjdk/samtools/metrics/MetricsFileTest.java | 213 -
.../samtools/reference/FastaSequenceFileTest.java | 85 -
.../samtools/reference/FastaSequenceIndexTest.java | 256 -
.../reference/IndexedFastaSequenceFileTest.java | 308 --
.../ReferenceSequenceFileFactoryTests.java | 39 -
.../reference/ReferenceSequenceFileWalkerTest.java | 73 -
.../seekablestream/SeekableBufferedStreamTest.java | 162 -
.../seekablestream/SeekableFileStreamTest.java | 52 -
.../seekablestream/SeekableStreamFactoryTest.java | 15 -
.../java/htsjdk/samtools/sra/SRAAccessionTest.java | 29 -
.../java/htsjdk/samtools/sra/SRAReferenceTest.java | 23 -
src/tests/java/htsjdk/samtools/sra/SRATest.java | 431 --
.../util/BlockCompressedOutputStreamTest.java | 112 -
.../util/BlockCompressedTerminatorTest.java | 59 -
.../java/htsjdk/samtools/util/HistogramTest.java | 97 -
.../htsjdk/samtools/util/IntelDeflaterTest.java | 130 -
.../htsjdk/samtools/util/IntervalListTest.java | 520 --
.../java/htsjdk/samtools/util/IoUtilTest.java | 190 -
.../samtools/util/QualityEncodingDetectorTest.java | 109 -
.../htsjdk/samtools/util/SamLocusIteratorTest.java | 231 -
src/tests/java/htsjdk/tribble/TestUtils.java | 28 -
.../htsjdk/tribble/index/IndexFactoryTest.java | 115 -
.../htsjdk/tribble/index/tabix/TabixIndexTest.java | 143 -
.../readers/AsynchronousLineReaderTest.java | 34 -
.../htsjdk/tribble/readers/LineReaderUtilTest.java | 27 -
.../htsjdk/variant/PrintVariantsExampleTest.java | 65 -
src/tests/java/htsjdk/variant/VariantBaseTest.java | 278 --
.../utils/SAMSequenceDictionaryExtractorTest.java | 65 -
.../GenotypeLikelihoodsUnitTest.java | 336 --
.../variantcontext/VariantContextTestProvider.java | 1017 ----
.../variantcontext/VariantContextUnitTest.java | 1450 ------
.../FilteringVariantContextIteratorTest.java | 88 -
.../filter/JavascriptVariantFilterTest.java | 72 -
.../writer/TabixOnTheFlyIndexCreationTest.java | 66 -
.../variantcontext/writer/VCFWriterUnitTest.java | 280 --
.../VariantContextWriterBuilderUnitTest.java | 377 --
.../htsjdk/variant/vcf/AbstractVCFCodecTest.java | 53 -
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 491 --
1387 files changed, 39826 insertions(+), 32670 deletions(-)
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