[med-svn] [htsjdk] branch upstream updated (ed6db4b -> 2329a1c)
Andreas Tille
tille at debian.org
Wed Oct 11 09:13:38 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository htsjdk.
from ed6db4b New upstream version 2.8.1+dfsg
new 2329a1c New upstream version 2.12.0+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.codecov.yml | 29 +
.travis.yml | 5 +-
README.md | 34 +-
build.gradle | 103 +-
gradle/wrapper/gradle-wrapper.properties | 4 +-
gradlew | 5 +
scripts/checkScalaAndJavaFiles.sh | 17 +
scripts/release_picard.sh | 152 -
settings.gradle | 1 +
.../java/htsjdk/samtools/AbstractBAMFileIndex.java | 3 +
.../htsjdk/samtools/AbstractSAMHeaderRecord.java | 12 +-
.../java/htsjdk/samtools/AsyncSAMFileWriter.java | 2 +
src/main/java/htsjdk/samtools/BAMFileReader.java | 265 +-
src/main/java/htsjdk/samtools/BAMFileSpan.java | 50 +-
src/main/java/htsjdk/samtools/BAMFileWriter.java | 35 +-
src/main/java/htsjdk/samtools/BAMIndex.java | 1 +
src/main/java/htsjdk/samtools/BAMIndexWriter.java | 1 +
src/main/java/htsjdk/samtools/BAMIndexer.java | 37 +-
src/main/java/htsjdk/samtools/BAMRecord.java | 8 +-
src/main/java/htsjdk/samtools/BAMRecordCodec.java | 12 +-
src/main/java/htsjdk/samtools/Bin.java | 1 +
src/main/java/htsjdk/samtools/BinList.java | 4 +
.../java/htsjdk/samtools/BinaryBAMIndexWriter.java | 14 +-
.../java/htsjdk/samtools/BinningIndexBuilder.java | 17 +-
.../java/htsjdk/samtools/BinningIndexContent.java | 4 +
.../htsjdk/samtools/CRAMContainerStreamWriter.java | 9 +-
src/main/java/htsjdk/samtools/CRAMFileReader.java | 12 +-
src/main/java/htsjdk/samtools/CRAMFileWriter.java | 4 +-
src/main/java/htsjdk/samtools/CRAMIterator.java | 4 +-
.../java/htsjdk/samtools/CachingBAMFileIndex.java | 4 +
src/main/java/htsjdk/samtools/Chunk.java | 2 +
src/main/java/htsjdk/samtools/CigarElement.java | 1 +
.../samtools/ComparableSamRecordIterator.java | 1 +
.../samtools/CoordinateSortedPairInfoMap.java | 5 +
.../htsjdk/samtools/DefaultSAMRecordFactory.java | 2 +
src/main/java/htsjdk/samtools/Defaults.java | 14 +-
.../htsjdk/samtools/DiskBasedBAMFileIndex.java | 2 +
.../htsjdk/samtools/DuplicateScoringStrategy.java | 40 +-
.../java/htsjdk/samtools/DuplicateSetIterator.java | 6 +-
src/main/java/htsjdk/samtools/FixBAMFile.java | 4 +
.../htsjdk/samtools/MergingSamRecordIterator.java | 7 +
src/main/java/htsjdk/samtools/QueryInterval.java | 27 +-
src/main/java/htsjdk/samtools/SAMFileHeader.java | 123 +-
src/main/java/htsjdk/samtools/SAMFileWriter.java | 1 +
.../java/htsjdk/samtools/SAMFileWriterFactory.java | 213 +-
.../java/htsjdk/samtools/SAMFileWriterImpl.java | 14 +-
.../java/htsjdk/samtools/SAMProgramRecord.java | 8 +
.../java/htsjdk/samtools/SAMReadGroupRecord.java | 7 +
src/main/java/htsjdk/samtools/SAMRecord.java | 199 +-
.../samtools/SAMRecordCoordinateComparator.java | 2 +
.../samtools/SAMRecordDuplicateComparator.java | 2 +
.../samtools/SAMRecordQueryNameComparator.java | 2 +
.../java/htsjdk/samtools/SAMRecordSetBuilder.java | 22 +-
src/main/java/htsjdk/samtools/SAMRecordUtil.java | 27 +-
.../htsjdk/samtools/SAMSequenceDictionary.java | 50 +-
.../java/htsjdk/samtools/SAMSequenceRecord.java | 14 +-
src/main/java/htsjdk/samtools/SAMTestUtil.java | 50 +-
.../java/htsjdk/samtools/SAMTextHeaderCodec.java | 48 +-
src/main/java/htsjdk/samtools/SAMTextReader.java | 20 +
src/main/java/htsjdk/samtools/SAMTextWriter.java | 4 +
src/main/java/htsjdk/samtools/SAMTools.java | 3 +
src/main/java/htsjdk/samtools/SAMUtils.java | 323 +-
.../java/htsjdk/samtools/SAMValidationError.java | 20 +-
.../java/htsjdk/samtools/SamFileHeaderMerger.java | 3 +
.../java/htsjdk/samtools/SamFileValidator.java | 100 +-
.../java/htsjdk/samtools/SamInputResource.java | 45 +-
src/main/java/htsjdk/samtools/SamPairUtil.java | 3 +
src/main/java/htsjdk/samtools/SamReader.java | 12 +-
.../java/htsjdk/samtools/SamReaderFactory.java | 75 +-
.../StreamInflatingIndexingOutputStream.java | 15 +-
src/main/java/htsjdk/samtools/TextTagCodec.java | 3 +
.../htsjdk/samtools/TextualBAMIndexWriter.java | 3 +
.../htsjdk/samtools/cram/build/CramNormalizer.java | 11 +-
.../samtools/cram/build/Sam2CramRecordFactory.java | 136 +-
.../cram/encoding/ByteArrayLenEncoding.java | 2 +
.../cram/encoding/ByteArrayStopEncoding.java | 2 +
.../cram/encoding/ExternalByteArrayEncoding.java | 2 +
.../cram/encoding/ExternalByteEncoding.java | 2 +
.../cram/encoding/ExternalIntegerEncoding.java | 2 +
.../cram/encoding/ExternalLongEncoding.java | 2 +
.../cram/encoding/GolombRiceIntegerCodec.java | 1 +
.../cram/encoding/huffman/HuffmanTree.java | 1 +
.../encoding/readfeatures/BaseQualityScore.java | 1 +
.../cram/encoding/readfeatures/HardClip.java | 2 +
.../cram/encoding/readfeatures/InsertBase.java | 2 +
.../cram/encoding/readfeatures/Insertion.java | 2 +
.../cram/encoding/readfeatures/Padding.java | 2 +
.../cram/encoding/readfeatures/ReadBase.java | 1 +
.../cram/encoding/readfeatures/RefSkip.java | 2 +
.../cram/encoding/readfeatures/SoftClip.java | 2 +
.../cram/encoding/readfeatures/Substitution.java | 17 +-
.../samtools/cram/io/CountingInputStream.java | 8 +
.../samtools/cram/io/DefaultBitInputStream.java | 4 +
.../samtools/cram/io/DefaultBitOutputStream.java | 4 +
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 26 +-
.../htsjdk/samtools/fastq/BasicFastqWriter.java | 10 +-
.../java/htsjdk/samtools/fastq/FastqConstants.java | 4 +-
.../java/htsjdk/samtools/fastq/FastqEncoder.java | 113 +
.../java/htsjdk/samtools/fastq/FastqReader.java | 56 +-
.../java/htsjdk/samtools/fastq/FastqRecord.java | 235 +-
.../java/htsjdk/samtools/fastq/FastqWriter.java | 1 +
.../htsjdk/samtools/filter/AggregateFilter.java | 2 +
.../java/htsjdk/samtools/filter/AlignedFilter.java | 2 +
.../samtools/filter/DuplicateReadFilter.java | 2 +
.../filter/FailsVendorReadQualityFilter.java | 2 +
.../htsjdk/samtools/filter/FilteringIterator.java | 2 +-
.../samtools/filter/FilteringSamIterator.java | 4 +
.../htsjdk/samtools/filter/IntervalFilter.java | 2 +
.../samtools/filter/IntervalKeepPairFilter.java | 2 +
.../samtools/filter/NotPrimaryAlignmentFilter.java | 2 +
.../htsjdk/samtools/filter/ReadNameFilter.java | 4 +-
.../samtools/filter/SecondaryAlignmentFilter.java | 2 +
.../filter/SecondaryOrSupplementaryFilter.java | 2 +
.../htsjdk/samtools/filter/SolexaNoiseFilter.java | 2 +
.../java/htsjdk/samtools/filter/TagFilter.java | 2 +
.../samtools/filter/WholeReadClippedFilter.java | 1 +
.../java/htsjdk/samtools/metrics/StringHeader.java | 1 +
.../htsjdk/samtools/metrics/VersionHeader.java | 1 +
.../reference/AbstractFastaSequenceFile.java | 31 +-
.../samtools/reference/FastaSequenceFile.java | 3 +
.../samtools/reference/FastaSequenceIndex.java | 27 +-
.../reference/FastaSequenceIndexCreator.java | 180 ++
.../reference/IndexedFastaSequenceFile.java | 14 +-
.../samtools/reference/ReferenceSequenceFile.java | 1 +
.../reference/ReferenceSequenceFileFactory.java | 71 +-
.../reference/ReferenceSequenceFileWalker.java | 5 +-
.../seekablestream/ByteArraySeekableStream.java | 23 +-
.../seekablestream/ISeekableStreamFactory.java | 22 +
.../seekablestream/SeekableBufferedStream.java | 6 +
.../samtools/seekablestream/SeekableFTPStream.java | 4 +
.../seekablestream/SeekableFileStream.java | 7 +
.../seekablestream/SeekableHTTPStream.java | 7 +
.../seekablestream/SeekablePathStream.java | 11 +-
.../samtools/seekablestream/SeekableStream.java | 2 +
.../seekablestream/SeekableStreamFactory.java | 23 +
.../java/htsjdk/samtools/sra/SRALazyRecord.java | 1 +
.../htsjdk/samtools/util/AbstractAsyncWriter.java | 5 +-
.../htsjdk/samtools/util/AbstractLocusInfo.java | 2 +
.../samtools/util/AbstractLocusIterator.java | 5 +
.../samtools/util/AbstractRecordAndOffset.java | 17 -
.../java/htsjdk/samtools/util/AsciiWriter.java | 3 +
.../util/AsyncBlockCompressedInputStream.java | 234 ++
.../java/htsjdk/samtools/util/BinaryCodec.java | 33 +-
.../samtools/util/BlockCompressedInputStream.java | 474 ++-
.../samtools/util/BlockCompressedOutputStream.java | 4 +-
.../java/htsjdk/samtools/util/BlockGunzipper.java | 35 +-
.../htsjdk/samtools/util/BufferedLineReader.java | 61 +-
.../htsjdk/samtools/util/CloseableIterator.java | 1 +
.../samtools/util/CustomGzipOutputStream.java | 4 +-
src/main/java/htsjdk/samtools/util/DateParser.java | 41 -
.../htsjdk/samtools/util/DelegatingIterator.java | 4 +
.../java/htsjdk/samtools/util/DiskBackedQueue.java | 3 +
.../samtools/util/EdgingRecordAndOffset.java | 4 +
.../java/htsjdk/samtools/util/FastLineReader.java | 1 +
.../samtools/util/FileAppendStreamLRUCache.java | 2 +
src/main/java/htsjdk/samtools/util/IOUtil.java | 81 +-
src/main/java/htsjdk/samtools/util/Interval.java | 1 +
.../java/htsjdk/samtools/util/IntervalList.java | 84 +-
.../util/IntervalListReferenceSequenceMask.java | 4 +
.../java/htsjdk/samtools/util/IntervalTree.java | 19 +-
.../java/htsjdk/samtools/util/IntervalTreeMap.java | 31 +-
.../java/htsjdk/samtools/util/Iso8601Date.java | 1 +
src/main/java/htsjdk/samtools/util/Lazy.java | 21 +-
src/main/java/htsjdk/samtools/util/LineReader.java | 1 +
src/main/java/htsjdk/samtools/util/Locatable.java | 54 +
.../java/htsjdk/samtools/util/LocusComparator.java | 1 +
src/main/java/htsjdk/samtools/util/LocusImpl.java | 2 +
src/main/java/htsjdk/samtools/util/Log.java | 35 +-
.../samtools/util/Md5CalculatingInputStream.java | 9 +
.../samtools/util/Md5CalculatingOutputStream.java | 17 +-
.../java/htsjdk/samtools/util/PeekIterator.java | 3 +
.../htsjdk/samtools/util/PeekableIterator.java | 4 +
.../samtools/util/PositionalOutputStream.java | 4 +
.../samtools/util/QualityEncodingDetector.java | 3 +
.../htsjdk/samtools/util/SamLocusIterator.java | 12 +-
.../util/SamRecordIntervalIteratorFactory.java | 4 +
.../java/htsjdk/samtools/util/SequenceUtil.java | 92 +-
.../java/htsjdk/samtools/util/SnappyLoader.java | 131 +-
.../htsjdk/samtools/util/SortingCollection.java | 14 +
.../samtools/util/SortingLongCollection.java | 1 +
.../htsjdk/samtools/util/StringLineReader.java | 71 +-
src/main/java/htsjdk/samtools/util/StringUtil.java | 6 +
.../htsjdk/samtools/util/TempStreamFactory.java | 4 +-
.../util/WholeGenomeReferenceSequenceMask.java | 4 +
.../htsjdk/samtools/util/zip/DeflaterFactory.java | 6 +-
.../{DeflaterFactory.java => InflaterFactory.java} | 25 +-
.../java/htsjdk/tribble/AbstractFeatureReader.java | 73 +-
.../java/htsjdk/tribble/AsciiFeatureCodec.java | 13 +-
src/main/java/htsjdk/tribble/Feature.java | 5 +-
src/main/java/htsjdk/tribble/FeatureCodec.java | 41 +-
src/main/java/htsjdk/tribble/FeatureReader.java | 1 +
src/main/java/htsjdk/tribble/SimpleFeature.java | 3 +
.../java/htsjdk/tribble/TabixFeatureReader.java | 42 +-
src/main/java/htsjdk/tribble/Tribble.java | 45 +-
src/main/java/htsjdk/tribble/TribbleException.java | 8 +
.../tribble/TribbleIndexedFeatureReader.java | 82 +-
src/main/java/htsjdk/tribble/bed/BEDCodec.java | 33 +-
.../java/htsjdk/tribble/bed/FullBEDFeature.java | 1 +
.../java/htsjdk/tribble/bed/SimpleBEDFeature.java | 10 +
.../java/htsjdk/tribble/example/CountRecords.java | 3 -
.../htsjdk/tribble/gelitext/DiploidGenotype.java | 66 -
.../htsjdk/tribble/gelitext/GeliTextCodec.java | 117 -
.../htsjdk/tribble/gelitext/GeliTextFeature.java | 148 -
.../java/htsjdk/tribble/index/AbstractIndex.java | 80 +-
.../htsjdk/tribble/index/DynamicIndexCreator.java | 25 +-
src/main/java/htsjdk/tribble/index/Index.java | 33 +-
.../java/htsjdk/tribble/index/IndexFactory.java | 115 +-
.../htsjdk/tribble/index/interval/Interval.java | 1 +
.../index/interval/IntervalIndexCreator.java | 21 +-
.../tribble/index/interval/IntervalTreeIndex.java | 16 +
.../htsjdk/tribble/index/linear/LinearIndex.java | 29 +-
.../tribble/index/linear/LinearIndexCreator.java | 19 +-
.../htsjdk/tribble/index/tabix/TabixFormat.java | 3 +-
.../htsjdk/tribble/index/tabix/TabixIndex.java | 31 +-
.../htsjdk/tribble/readers/AsciiLineReader.java | 131 +-
.../readers/BlockCompressedAsciiLineReader.java | 44 +
.../java/htsjdk/tribble/readers/LineReader.java | 1 +
.../htsjdk/tribble/readers/LineReaderUtil.java | 56 -
.../tribble/readers/LongLineBufferedReader.java | 8 +
.../tribble/readers/PositionalBufferedStream.java | 9 +-
.../tribble/readers/TabixIteratorLineReader.java | 2 +
.../java/htsjdk/tribble/readers/TabixReader.java | 136 +-
src/main/java/htsjdk/tribble/util/HTTPHelper.java | 8 +
.../tribble/util/LittleEndianOutputStream.java | 2 +
.../java/htsjdk/tribble/util/ParsingUtils.java | 30 +-
src/main/java/htsjdk/tribble/util/TabixUtils.java | 1 +
src/main/java/htsjdk/variant/bcf2/BCF2Codec.java | 21 +-
.../java/htsjdk/variant/variantcontext/Allele.java | 1 +
.../variant/variantcontext/FastGenotype.java | 1 +
.../variantcontext/GenotypeLikelihoods.java | 6 +
.../htsjdk/variant/variantcontext/JEXLMap.java | 12 +
.../variant/variantcontext/VariantContext.java | 2 +
.../variantcontext/VariantContextUtils.java | 15 +-
.../variant/variantcontext/VariantJEXLContext.java | 3 +
.../variantcontext/filter/FilteringIterator.java | 2 +-
.../writer/AsyncVariantContextWriter.java | 8 +
.../variantcontext/writer/BCF2FieldWriter.java | 1 +
.../variant/variantcontext/writer/BCF2Writer.java | 69 +-
.../writer/IndexingVariantContextWriter.java | 7 +-
.../writer/SortingVariantContextWriter.java | 5 +
.../writer/SortingVariantContextWriterBase.java | 12 +-
.../variant/variantcontext/writer/VCFWriter.java | 25 +-
.../writer/VariantContextWriter.java | 18 +
.../writer/VariantContextWriterBuilder.java | 6 +-
.../writer/VariantContextWriterFactory.java | 282 --
.../java/htsjdk/variant/vcf/AbstractVCFCodec.java | 13 +-
src/main/java/htsjdk/variant/vcf/VCF3Codec.java | 2 +
src/main/java/htsjdk/variant/vcf/VCFCodec.java | 1 +
.../htsjdk/variant/vcf/VCFCompoundHeaderLine.java | 2 +
src/main/java/htsjdk/variant/vcf/VCFEncoder.java | 715 ++--
.../java/htsjdk/variant/vcf/VCFFileReader.java | 15 +-
src/main/java/htsjdk/variant/vcf/VCFHeader.java | 26 +-
.../java/htsjdk/variant/vcf/VCFHeaderLine.java | 1 +
.../variant/vcf/VCFHeaderLineTranslator.java | 2 +
.../htsjdk/variant/vcf/VCFSimpleHeaderLine.java | 2 +
src/main/java/htsjdk/variant/vcf/VCFUtils.java | 10 +-
src/test/java/htsjdk/HtsjdkTest.java | 10 +
.../htsjdk/cram/io/ExternalCompressionTest.java | 9 +-
.../htsjdk/samtools/AbstractBAMFileIndexTest.java | 5 +-
.../java/htsjdk/samtools/BAMCigarOverflowTest.java | 3 +-
.../java/htsjdk/samtools/BAMFileIndexTest.java | 21 +-
src/test/java/htsjdk/samtools/BAMFileSpanTest.java | 72 +
.../java/htsjdk/samtools/BAMFileWriterTest.java | 42 +-
.../java/htsjdk/samtools/BAMIndexWriterTest.java | 9 +-
src/test/java/htsjdk/samtools/BAMIteratorTest.java | 3 +-
...AMQueryMultipleIntervalsIteratorFilterTest.java | 3 +-
.../java/htsjdk/samtools/BAMRemoteFileTest.java | 3 +-
src/test/java/htsjdk/samtools/BinTest.java | 3 +-
.../htsjdk/samtools/BinningIndexBuilderTest.java | 105 +
.../java/htsjdk/samtools/CRAMBAIIndexerTest.java | 3 +-
.../java/htsjdk/samtools/CRAMCRAIIndexerTest.java | 9 +-
.../java/htsjdk/samtools/CRAMComplianceTest.java | 328 +-
.../samtools/CRAMContainerStreamWriterTest.java | 3 +-
.../java/htsjdk/samtools/CRAMEdgeCasesTest.java | 3 +-
.../java/htsjdk/samtools/CRAMFileBAIIndexTest.java | 3 +-
.../htsjdk/samtools/CRAMFileCRAIIndexTest.java | 4 +-
.../java/htsjdk/samtools/CRAMFileReaderTest.java | 5 +-
.../java/htsjdk/samtools/CRAMFileWriterTest.java | 4 +-
.../samtools/CRAMFileWriterWithIndexTest.java | 3 +-
.../java/htsjdk/samtools/CRAMIndexQueryTest.java | 9 +-
.../java/htsjdk/samtools/CRAMSliceMD5Test.java | 136 +
src/test/java/htsjdk/samtools/ChunkTest.java | 3 +-
src/test/java/htsjdk/samtools/CigarCodecTest.java | 3 +-
.../htsjdk/samtools/CigarOperatorUnitTest.java | 137 +
src/test/java/htsjdk/samtools/CigarTest.java | 129 +-
.../htsjdk/samtools/DownsamplingIteratorTests.java | 3 +-
.../samtools/DuplicateScoringStrategyTest.java | 26 +
.../htsjdk/samtools/DuplicateSetIteratorTest.java | 3 +-
.../java/htsjdk/samtools/GenomicIndexUtilTest.java | 5 +-
...MergingSamRecordIteratorGroupCollisionTest.java | 19 +-
.../samtools/MergingSamRecordIteratorTest.java | 3 +-
.../htsjdk/samtools/PathInputResourceTest.java | 48 +
.../htsjdk/samtools/ProgramRecordChainingTest.java | 3 +-
.../java/htsjdk/samtools/QueryIntervalTest.java | 42 +
.../samtools/SAMBinaryTagAndValueUnitTest.java | 3 +-
src/test/java/htsjdk/samtools/SAMCloneTest.java | 3 +-
.../java/htsjdk/samtools/SAMFileHeaderTest.java | 64 +
.../htsjdk/samtools/SAMFileWriterFactoryTest.java | 142 +-
src/test/java/htsjdk/samtools/SAMFlagTest.java | 3 +-
.../java/htsjdk/samtools/SAMIntegerTagTest.java | 3 +-
.../{BinTest.java => SAMProgramRecordTest.java} | 20 +-
.../htsjdk/samtools/SAMReadGroupRecordTest.java | 148 +
.../samtools/SAMRecordDuplicateComparatorTest.java | 3 +-
....java => SAMRecordQueryHashComparatorTest.java} | 50 +-
.../samtools/SAMRecordQueryNameComparatorTest.java | 124 +
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 76 +-
.../samtools/SAMSequenceDictionaryCodecTest.java | 17 +-
.../htsjdk/samtools/SAMSequenceDictionaryTest.java | 36 +-
.../htsjdk/samtools/SAMSequenceRecordTest.java | 86 +
.../java/htsjdk/samtools/SAMTextReaderTest.java | 3 +-
.../java/htsjdk/samtools/SAMTextWriterTest.java | 3 +-
src/test/java/htsjdk/samtools/SAMUtilsTest.java | 39 +-
.../htsjdk/samtools/SamFileHeaderMergerTest.java | 3 +-
src/test/java/htsjdk/samtools/SamFilesTest.java | 4 +-
.../java/htsjdk/samtools/SamFlagFieldTest.java | 5 +-
.../samtools/SamHeaderRecordComparatorTest.java | 3 +-
src/test/java/htsjdk/samtools/SamIndexesTest.java | 3 +-
src/test/java/htsjdk/samtools/SamPairUtilTest.java | 3 +-
.../java/htsjdk/samtools/SamReaderFactoryTest.java | 77 +-
.../java/htsjdk/samtools/SamReaderSortTest.java | 61 +-
src/test/java/htsjdk/samtools/SamReaderTest.java | 6 +-
src/test/java/htsjdk/samtools/SamSpecIntTest.java | 3 +-
src/test/java/htsjdk/samtools/SamStreamsTest.java | 5 +-
.../samtools/SeekableByteChannelFromBuffer.java | 85 +
.../SequenceNameTruncationAndValidationTest.java | 3 +-
.../java/htsjdk/samtools/ValidateSamFileTest.java | 77 +-
.../java/htsjdk/samtools/cram/CRAIEntryTest.java | 3 +-
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 17 +-
.../samtools/cram/LosslessRoundTripTest.java | 21 +-
.../java/htsjdk/samtools/cram/VersionTest.java | 3 +-
.../cram/build/CompressionHeaderFactoryTest.java | 3 +-
.../samtools/cram/build/ContainerFactoryTest.java | 3 +-
.../samtools/cram/build/ContainerParserTest.java | 3 +-
.../htsjdk/samtools/cram/build/CramIOTest.java | 3 +-
.../cram/build/Sam2CramRecordFactoryTest.java | 109 +
.../cram/encoding/huffman/codec/HuffmanTest.java | 3 +-
.../samtools/cram/encoding/rans/RansTest.java | 3 +-
.../java/htsjdk/samtools/cram/io/ITF8Test.java | 3 +-
.../java/htsjdk/samtools/cram/io/LTF8Test.java | 3 +-
.../cram/lossy/QualityScorePreservationTest.java | 9 +-
.../samtools/cram/ref/EnaRefServiceTest.java | 3 +-
.../samtools/cram/ref/ReferenceSourceTest.java | 33 +
.../cram/structure/CramCompressionRecordTest.java | 9 +-
.../samtools/cram/structure/ReadTagTest.java | 10 +-
.../htsjdk/samtools/cram/structure/SliceTests.java | 4 +-
.../cram/structure/SubstitutionMatrixTest.java | 6 +-
.../htsjdk/samtools/fastq/FastqEncoderTest.java | 76 +
.../htsjdk/samtools/fastq/FastqRecordTest.java | 31 +-
.../htsjdk/samtools/fastq/FastqWriterTest.java | 73 -
.../filter/FailsVendorReadQualityFilterTest.java | 3 +-
.../samtools/filter/InsertSizeFilterTest.java | 3 +-
.../htsjdk/samtools/filter/IntervalFilterTest.java | 96 +
.../filter/IntervalKeepPairFilterTest.java | 3 +-
.../filter/JavascriptSamRecordFilterTest.java | 3 +-
.../samtools/filter/MappingQualityFilterTest.java | 3 +-
.../filter/NotPrimaryAlignmentFilterTest.java | 109 +
.../samtools/filter/OverclippedReadFilterTest.java | 3 +-
.../htsjdk/samtools/filter/ReadNameFilterTest.java | 52 +
.../filter/SecondaryOrSupplementaryFilterTest.java | 107 +
.../samtools/filter/SolexaNoiseFilterTest.java | 3 +-
.../java/htsjdk/samtools/filter/TagFilterTest.java | 5 +-
.../htsjdk/samtools/liftover/LiftOverTest.java | 3 +-
.../htsjdk/samtools/metrics/MetricBaseTest.java | 3 +-
.../htsjdk/samtools/metrics/MetricsFileTest.java | 3 +-
.../htsjdk/samtools/metrics/StringHeaderTest.java | 5 +-
.../htsjdk/samtools/metrics/VersionHeaderTest.java | 5 +-
.../samtools/reference/FastaSequenceFileTest.java | 3 +-
.../reference/FastaSequenceIndexCreatorTest.java | 90 +
.../samtools/reference/FastaSequenceIndexTest.java | 35 +-
.../reference/IndexedFastaSequenceFileTest.java | 3 +-
.../ReferenceSequenceFileFactoryTests.java | 21 +-
.../reference/ReferenceSequenceFileWalkerTest.java | 3 +-
.../samtools/reference/ReferenceSequenceTests.java | 3 +-
.../ByteArraySeekableStreamTest.java | 116 +
.../seekablestream/SeekableBufferedStreamTest.java | 3 +-
.../seekablestream/SeekableFTPStreamTest.java | 3 +-
.../seekablestream/SeekableFileStreamTest.java | 3 +-
.../seekablestream/SeekableMemoryStreamTest.java | 3 +-
.../seekablestream/SeekablePathStreamTest.java | 4 +-
.../seekablestream/SeekableStreamFactoryTest.java | 3 +-
.../java/htsjdk/samtools/sra/AbstractSRATest.java | 7 +-
.../samtools/util/AbstractLocusInfoTest.java | 5 +-
.../util/AbstractLocusIteratorTestTemplate.java | 5 +-
.../samtools/util/AbstractRecordAndOffsetTest.java | 14 +-
.../util/AsyncBlockCompressedInputStreamTest.java | 92 +
.../samtools/util/AsyncBufferedIteratorTest.java | 13 +-
.../java/htsjdk/samtools/util/AsyncWriterTest.java | 3 +-
.../java/htsjdk/samtools/util/BinaryCodecTest.java | 3 +-
.../util/BlockCompressedFilePointerUtilTest.java | 4 +-
.../util/BlockCompressedInputStreamTest.java | 201 ++
.../util/BlockCompressedOutputStreamTest.java | 32 +-
.../util/BlockCompressedTerminatorTest.java | 90 +-
...ReaderTest.java => BufferedLineReaderTest.java} | 53 +-
.../htsjdk/samtools/util/CigarElementUnitTest.java | 43 +
.../java/htsjdk/samtools/util/CigarUtilTest.java | 3 +-
.../samtools/util/CloseableIteratorTest.java | 3 +-
.../java/htsjdk/samtools/util/CodeUtilTest.java | 3 +-
.../htsjdk/samtools/util/ComparableTupleTest.java | 3 +-
.../samtools/util/CoordSpanInputSteamTest.java | 3 +-
.../java/htsjdk/samtools/util/DateParserTest.java | 151 +
.../htsjdk/samtools/util/DiskBackedQueueTest.java | 3 +
.../htsjdk/samtools/util/EdgeReadIteratorTest.java | 20 +-
.../samtools/util/EdgingRecordAndOffsetTest.java | 34 +-
.../java/htsjdk/samtools/util/HistogramTest.java | 3 +-
.../htsjdk/samtools/util/IntervalListTest.java | 115 +-
.../htsjdk/samtools/util/IntervalTreeMapTest.java | 7 +-
.../htsjdk/samtools/util/IntervalTreeTest.java | 158 +-
src/test/java/htsjdk/samtools/util/IoUtilTest.java | 31 +-
.../java/htsjdk/samtools/util/Iso8601DateTest.java | 3 +-
src/test/java/htsjdk/samtools/util/IupacTest.java | 3 +-
.../htsjdk/samtools/util/LocatableUnitTest.java | 160 +
src/test/java/htsjdk/samtools/util/LogTest.java | 41 +
.../htsjdk/samtools/util/MergingIteratorTest.java | 3 +-
.../htsjdk/samtools/util/OverlapDetectorTest.java | 3 +-
.../samtools/util/PositionalOutputStreamTest.java | 7 +-
.../samtools/util/QualityEncodingDetectorTest.java | 3 +-
.../samtools/util/RelativeIso8601DateTest.java | 3 +-
.../htsjdk/samtools/util/SamLocusIteratorTest.java | 44 +-
.../htsjdk/samtools/util/SequenceUtilTest.java | 187 +-
.../htsjdk/samtools/util/SnappyLoaderUnitTest.java | 49 +
.../samtools/util/SolexaQualityConverterTest.java | 3 +-
.../samtools/util/SortingCollectionTest.java | 13 +-
.../samtools/util/SortingLongCollectionTest.java | 3 +-
.../java/htsjdk/samtools/util/StringUtilTest.java | 122 -
.../htsjdk/samtools/util/TrimmingUtilTest.java | 3 +-
src/test/java/htsjdk/samtools/util/TupleTest.java | 5 +-
.../htsjdk/tribble/AbstractFeatureReaderTest.java | 169 +-
.../java/htsjdk/tribble/AsciiFeatureCodecTest.java | 35 +
.../java/htsjdk/tribble/BinaryFeaturesTest.java | 3 +-
.../java/htsjdk/tribble/FeatureReaderTest.java | 3 +-
.../tribble/TribbleIndexFeatureReaderTest.java | 53 +-
src/test/java/htsjdk/tribble/TribbleTest.java | 3 +-
src/test/java/htsjdk/tribble/bed/BEDCodecTest.java | 67 +-
.../java/htsjdk/tribble/gelitext/GeliTextTest.java | 100 -
.../htsjdk/tribble/index/IndexFactoryTest.java | 131 +-
src/test/java/htsjdk/tribble/index/IndexTest.java | 50 +-
.../tribble/index/interval/IntervalTreeTest.java | 3 +-
.../tribble/index/linear/LinearIndexTest.java | 3 +-
.../htsjdk/tribble/index/tabix/TabixIndexTest.java | 96 +-
.../tribble/readers/AsciiLineReaderTest.java | 65 +-
.../BlockCompressedAsciiLineReaderTest.java | 76 +
.../readers/LongLineBufferedReaderTest.java | 3 +-
.../readers/PositionalBufferedStreamTest.java | 3 +-
.../java/htsjdk/tribble/readers/ReaderTest.java | 3 +-
.../readers/SynchronousLineReaderUnitTest.java | 3 +-
.../htsjdk/tribble/readers/TabixReaderTest.java | 26 +-
.../java/htsjdk/tribble/util/ParsingUtilsTest.java | 64 +-
.../htsjdk/tribble/util/ftp/FTPClientTest.java | 3 +-
.../java/htsjdk/tribble/util/ftp/FTPUtilsTest.java | 3 +-
.../util/popgen/HardyWeinbergCalculationTest.java | 3 +-
.../htsjdk/variant/PrintVariantsExampleTest.java | 5 +-
src/test/java/htsjdk/variant/VariantBaseTest.java | 3 +-
.../htsjdk/variant/bcf2/BCF2WriterUnitTest.java | 282 ++
.../utils/SAMSequenceDictionaryExtractorTest.java | 3 +-
.../variantcontext/VariantContextTestProvider.java | 5 +-
.../variantcontext/VariantContextUnitTest.java | 89 +-
.../variantcontext/filter/CompoundFilterTest.java | 5 +-
.../FilteringVariantContextIteratorTest.java | 3 +-
.../filter/GenotypeQualityFilterTest.java | 3 +-
.../filter/HeterozygosityFilterTest.java | 3 +-
.../filter/JavascriptVariantFilterTest.java | 3 +-
.../filter/PassingVariantFilterTest.java | 5 +-
.../variantcontext/filter/SnpFilterTest.java | 3 +-
.../writer/AsyncVariantContextWriterUnitTest.java | 146 +
.../writer/TabixOnTheFlyIndexCreationTest.java | 3 +-
.../variantcontext/writer/VCFWriterUnitTest.java | 116 +-
.../VariantContextWriterBuilderUnitTest.java | 8 +
.../java/htsjdk/variant/vcf/VCFEncoderTest.java | 3 +-
.../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java | 56 +-
.../SequenceUtil/upper_and_lowercase_read.sam | 2 +-
.../ValidateSamFileTest/nm_tag_validation.cram | Bin 0 -> 39392 bytes
.../ValidateSamFileTest/nm_tag_validation.fa | 71 +
.../ValidateSamFileTest/nm_tag_validation.fa.fai | 1 +
.../{valid.sam => seq_qual_len_mismatch.sam} | 16 +-
...CEUTrio.HiSeq.WGS.b37.NA12878.20.first.8000.bam | Bin 0 -> 997323 bytes
.../cram/{c1#bounds.2.1.cram => amb#amb.2.1.cram} | Bin 10508 -> 11045 bytes
.../htsjdk/samtools/cram/amb#amb.3.0.cram | Bin 0 -> 1210 bytes
.../resources/htsjdk/samtools/cram/amb#amb.sam | 57 +
src/test/resources/htsjdk/samtools/cram/amb.fa | 2 +
src/test/resources/htsjdk/samtools/cram/amb.fa.fai | 1 +
.../htsjdk/samtools/cram/ambiguityCodes.fasta | 2 +
.../htsjdk/samtools/cram/ambiguityCodes.fasta.fai | 1 +
.../resources/htsjdk/samtools/cram/fieldarith.sam | 15 -
.../samtools/cram/human_g1k_v37.20.subset.dict | 2 +
.../samtools/cram/human_g1k_v37.20.subset.fasta | 151 +
.../cram/human_g1k_v37.20.subset.fasta.fai | 1 +
.../samtoolsSliceMD5WithAmbiguityCodesTest.cram | Bin 0 -> 1826 bytes
src/test/resources/htsjdk/samtools/cram/test.dict | 2 -
src/test/resources/htsjdk/samtools/cram/test.fa | 2 -
.../resources/htsjdk/samtools/cram/test.fa.fai | 1 -
src/test/resources/htsjdk/samtools/cram/test2.dict | 2 -
src/test/resources/htsjdk/samtools/cram/test2.fa | 2 -
.../resources/htsjdk/samtools/cram/test2.fa.fai | 1 -
.../resources/htsjdk/samtools/filter/names.txt | 3 +
.../samtools/{uncompressed.sam => noheader.sam} | 5 -
.../Homo_sapiens_assembly18.trimmed.fasta.gz | Bin 0 -> 335008 bytes
...> Homo_sapiens_assembly18.trimmed.fasta.gz.fai} | 0
.../Homo_sapiens_assembly18.trimmed.fasta.gz.gzi | Bin 0 -> 264 bytes
.../resources/htsjdk/samtools/reference/crlf.fasta | 4 +
.../htsjdk/samtools/reference/crlf.fasta.fai | 2 +
.../reference/header_with_white_space.fasta | 4 +
.../reference/header_with_white_space.fasta.fai | 2 +
src/test/resources/htsjdk/samtools/util/random.bin | Bin 0 -> 131072 bytes
.../resources/htsjdk/samtools/util/random.bin.gz | Bin 0 -> 131254 bytes
.../baseVariants.mangled.vcf.gz | Bin 0 -> 517 bytes
.../baseVariants.mangled.vcf.gz.tbi | Bin 0 -> 155 bytes
.../AbstractFeatureReaderTest/baseVariants.vcf | 37 +
.../AbstractFeatureReaderTest/baseVariants.vcf.gz | Bin 0 -> 516 bytes
.../baseVariants.vcf.gz.tbi | Bin 0 -> 154 bytes
.../AbstractFeatureReaderTest/baseVariants.vcf.idx | Bin 0 -> 507 bytes
.../corruptedBaseVariants.vcf.idx | Bin 0 -> 529 bytes
.../mangledBaseVariants.vcf | 37 +
.../mangledBaseVariants.vcf.idx | Bin 0 -> 509 bytes
.../htsjdk/tribble/bed/2featuresNoHeader.bed.gz | Bin 0 -> 73 bytes
.../tribble/bed/2featuresNoHeader.bed.gz.tbi | Bin 0 -> 123 bytes
.../htsjdk/tribble/bed/2featuresWithHeader.bed.gz | Bin 0 -> 81 bytes
.../tribble/bed/2featuresWithHeader.bed.gz.tbi | Bin 0 -> 124 bytes
.../htsjdk/tribble/bed/3featuresNoHeader.bed.gz | Bin 0 -> 78 bytes
.../tribble/bed/3featuresNoHeader.bed.gz.tbi | Bin 0 -> 123 bytes
.../htsjdk/tribble/bed/Unigene.sample.bed.gz | Bin 0 -> 3908 bytes
.../htsjdk/tribble/tabix/4featuresHG38Header.vcf | 3412 ++++++++++++++++++++
.../tribble/tabix/4featuresHG38Header.vcf.gz | Bin 0 -> 25163 bytes
.../tribble/tabix/4featuresHG38Header.vcf.gz.tbi | Bin 0 -> 258 bytes
src/test/scala/htsjdk/UnitSpec.scala | 25 +
.../samtools/fastq/FastqReaderWriterTest.scala | 180 ++
.../htsjdk/samtools/util/StringUtilTest.scala | 134 +
526 files changed, 15157 insertions(+), 3957 deletions(-)
create mode 100644 .codecov.yml
create mode 100755 scripts/checkScalaAndJavaFiles.sh
delete mode 100755 scripts/release_picard.sh
create mode 100644 settings.gradle
create mode 100644 src/main/java/htsjdk/samtools/fastq/FastqEncoder.java
create mode 100644 src/main/java/htsjdk/samtools/reference/FastaSequenceIndexCreator.java
create mode 100644 src/main/java/htsjdk/samtools/util/AsyncBlockCompressedInputStream.java
copy src/main/java/htsjdk/samtools/util/zip/{DeflaterFactory.java => InflaterFactory.java} (64%)
delete mode 100644 src/main/java/htsjdk/tribble/gelitext/DiploidGenotype.java
delete mode 100644 src/main/java/htsjdk/tribble/gelitext/GeliTextCodec.java
delete mode 100644 src/main/java/htsjdk/tribble/gelitext/GeliTextFeature.java
create mode 100644 src/main/java/htsjdk/tribble/readers/BlockCompressedAsciiLineReader.java
delete mode 100644 src/main/java/htsjdk/tribble/readers/LineReaderUtil.java
delete mode 100644 src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterFactory.java
create mode 100644 src/test/java/htsjdk/HtsjdkTest.java
create mode 100644 src/test/java/htsjdk/samtools/BAMFileSpanTest.java
create mode 100644 src/test/java/htsjdk/samtools/BinningIndexBuilderTest.java
create mode 100644 src/test/java/htsjdk/samtools/CRAMSliceMD5Test.java
create mode 100644 src/test/java/htsjdk/samtools/CigarOperatorUnitTest.java
create mode 100644 src/test/java/htsjdk/samtools/DuplicateScoringStrategyTest.java
create mode 100644 src/test/java/htsjdk/samtools/PathInputResourceTest.java
create mode 100644 src/test/java/htsjdk/samtools/QueryIntervalTest.java
create mode 100644 src/test/java/htsjdk/samtools/SAMFileHeaderTest.java
copy src/test/java/htsjdk/samtools/{BinTest.java => SAMProgramRecordTest.java} (69%)
create mode 100644 src/test/java/htsjdk/samtools/SAMReadGroupRecordTest.java
copy src/test/java/htsjdk/samtools/{util/PositionalOutputStreamTest.java => SAMRecordQueryHashComparatorTest.java} (51%)
create mode 100644 src/test/java/htsjdk/samtools/SAMRecordQueryNameComparatorTest.java
create mode 100644 src/test/java/htsjdk/samtools/SAMSequenceRecordTest.java
create mode 100644 src/test/java/htsjdk/samtools/SeekableByteChannelFromBuffer.java
create mode 100644 src/test/java/htsjdk/samtools/cram/build/Sam2CramRecordFactoryTest.java
create mode 100644 src/test/java/htsjdk/samtools/cram/ref/ReferenceSourceTest.java
create mode 100644 src/test/java/htsjdk/samtools/fastq/FastqEncoderTest.java
delete mode 100644 src/test/java/htsjdk/samtools/fastq/FastqWriterTest.java
create mode 100644 src/test/java/htsjdk/samtools/filter/IntervalFilterTest.java
create mode 100644 src/test/java/htsjdk/samtools/filter/NotPrimaryAlignmentFilterTest.java
create mode 100644 src/test/java/htsjdk/samtools/filter/ReadNameFilterTest.java
create mode 100644 src/test/java/htsjdk/samtools/filter/SecondaryOrSupplementaryFilterTest.java
create mode 100644 src/test/java/htsjdk/samtools/reference/FastaSequenceIndexCreatorTest.java
create mode 100644 src/test/java/htsjdk/samtools/seekablestream/ByteArraySeekableStreamTest.java
create mode 100644 src/test/java/htsjdk/samtools/util/AsyncBlockCompressedInputStreamTest.java
create mode 100644 src/test/java/htsjdk/samtools/util/BlockCompressedInputStreamTest.java
rename src/test/java/htsjdk/samtools/util/{StringLineReaderTest.java => BufferedLineReaderTest.java} (73%)
create mode 100644 src/test/java/htsjdk/samtools/util/CigarElementUnitTest.java
create mode 100644 src/test/java/htsjdk/samtools/util/DateParserTest.java
create mode 100644 src/test/java/htsjdk/samtools/util/LocatableUnitTest.java
create mode 100644 src/test/java/htsjdk/samtools/util/LogTest.java
create mode 100644 src/test/java/htsjdk/samtools/util/SnappyLoaderUnitTest.java
delete mode 100644 src/test/java/htsjdk/samtools/util/StringUtilTest.java
create mode 100644 src/test/java/htsjdk/tribble/AsciiFeatureCodecTest.java
delete mode 100644 src/test/java/htsjdk/tribble/gelitext/GeliTextTest.java
create mode 100644 src/test/java/htsjdk/tribble/readers/BlockCompressedAsciiLineReaderTest.java
create mode 100644 src/test/java/htsjdk/variant/bcf2/BCF2WriterUnitTest.java
create mode 100644 src/test/java/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriterUnitTest.java
create mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.cram
create mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa
create mode 100644 src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa.fai
copy src/test/resources/htsjdk/samtools/ValidateSamFileTest/{valid.sam => seq_qual_len_mismatch.sam} (82%)
create mode 100644 src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.first.8000.bam
copy src/test/resources/htsjdk/samtools/cram/{c1#bounds.2.1.cram => amb#amb.2.1.cram} (90%)
create mode 100644 src/test/resources/htsjdk/samtools/cram/amb#amb.3.0.cram
create mode 100644 src/test/resources/htsjdk/samtools/cram/amb#amb.sam
create mode 100644 src/test/resources/htsjdk/samtools/cram/amb.fa
create mode 100644 src/test/resources/htsjdk/samtools/cram/amb.fa.fai
create mode 100644 src/test/resources/htsjdk/samtools/cram/ambiguityCodes.fasta
create mode 100644 src/test/resources/htsjdk/samtools/cram/ambiguityCodes.fasta.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/fieldarith.sam
create mode 100644 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.dict
create mode 100644 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta
create mode 100644 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta.fai
create mode 100644 src/test/resources/htsjdk/samtools/cram/samtoolsSliceMD5WithAmbiguityCodesTest.cram
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test.dict
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test.fa.fai
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test2.dict
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test2.fa
delete mode 100644 src/test/resources/htsjdk/samtools/cram/test2.fa.fai
create mode 100644 src/test/resources/htsjdk/samtools/filter/names.txt
copy src/test/resources/htsjdk/samtools/{uncompressed.sam => noheader.sam} (85%)
mode change 100644 => 100755
create mode 100644 src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz
copy src/test/resources/htsjdk/samtools/reference/{Homo_sapiens_assembly18.trimmed.fasta.fai => Homo_sapiens_assembly18.trimmed.fasta.gz.fai} (100%)
create mode 100644 src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz.gzi
create mode 100644 src/test/resources/htsjdk/samtools/reference/crlf.fasta
create mode 100644 src/test/resources/htsjdk/samtools/reference/crlf.fasta.fai
create mode 100644 src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta
create mode 100644 src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta.fai
create mode 100644 src/test/resources/htsjdk/samtools/util/random.bin
create mode 100644 src/test/resources/htsjdk/samtools/util/random.bin.gz
create mode 100644 src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.mangled.vcf.gz
create mode 100644 src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.mangled.vcf.gz.tbi
create mode 100644 src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf
create mode 100644 src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf.gz
create mode 100644 src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf.gz.tbi
create mode 100644 src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/baseVariants.vcf.idx
create mode 100644 src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/corruptedBaseVariants.vcf.idx
create mode 100644 src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/mangledBaseVariants.vcf
create mode 100644 src/test/resources/htsjdk/tribble/AbstractFeatureReaderTest/mangledBaseVariants.vcf.idx
create mode 100644 src/test/resources/htsjdk/tribble/bed/2featuresNoHeader.bed.gz
create mode 100644 src/test/resources/htsjdk/tribble/bed/2featuresNoHeader.bed.gz.tbi
create mode 100644 src/test/resources/htsjdk/tribble/bed/2featuresWithHeader.bed.gz
create mode 100644 src/test/resources/htsjdk/tribble/bed/2featuresWithHeader.bed.gz.tbi
create mode 100644 src/test/resources/htsjdk/tribble/bed/3featuresNoHeader.bed.gz
create mode 100644 src/test/resources/htsjdk/tribble/bed/3featuresNoHeader.bed.gz.tbi
create mode 100644 src/test/resources/htsjdk/tribble/bed/Unigene.sample.bed.gz
create mode 100644 src/test/resources/htsjdk/tribble/tabix/4featuresHG38Header.vcf
create mode 100644 src/test/resources/htsjdk/tribble/tabix/4featuresHG38Header.vcf.gz
create mode 100644 src/test/resources/htsjdk/tribble/tabix/4featuresHG38Header.vcf.gz.tbi
create mode 100644 src/test/scala/htsjdk/UnitSpec.scala
create mode 100644 src/test/scala/htsjdk/samtools/fastq/FastqReaderWriterTest.scala
create mode 100644 src/test/scala/htsjdk/samtools/util/StringUtilTest.scala
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