You can download htsjdk-1.128.jar in this page.
MIT License
htsjdk-1.128.jar file has the following types.
META-INF/MANIFEST.MF htsjdk.samtools.AbstractBAMFileIndex.class htsjdk.samtools.AbstractSAMHeaderRecord.class htsjdk.samtools.AlignmentBlock.class htsjdk.samtools.AsyncSAMFileWriter.class htsjdk.samtools.BAMFileConstants.class htsjdk.samtools.BAMFileReader.class htsjdk.samtools.BAMFileSpan.class htsjdk.samtools.BAMFileWriter.class htsjdk.samtools.BAMIndex.class htsjdk.samtools.BAMIndexContent.class htsjdk.samtools.BAMIndexMetaData.class htsjdk.samtools.BAMIndexWriter.class htsjdk.samtools.BAMIndexer.class htsjdk.samtools.BAMRecord.class htsjdk.samtools.BAMRecordCodec.class htsjdk.samtools.BamFileIoUtils.class htsjdk.samtools.BamIndexValidator.class htsjdk.samtools.Bin.class htsjdk.samtools.BinList.class htsjdk.samtools.BinaryBAMIndexWriter.class htsjdk.samtools.BinaryCigarCodec.class htsjdk.samtools.BinaryTagCodec.class htsjdk.samtools.BinningIndexBuilder.class htsjdk.samtools.BinningIndexContent.class htsjdk.samtools.BrowseableBAMIndex.class htsjdk.samtools.CRAMFileReader.class htsjdk.samtools.CRAMFileWriter.class htsjdk.samtools.CRAMIndexer.class htsjdk.samtools.CRAMIterator.class htsjdk.samtools.CachingBAMFileIndex.class htsjdk.samtools.Chunk.class htsjdk.samtools.Cigar.class htsjdk.samtools.CigarElement.class htsjdk.samtools.CigarOperator.class htsjdk.samtools.ComparableSamRecordIterator.class htsjdk.samtools.CoordinateSortedPairInfoMap.class htsjdk.samtools.CustomReaderFactory.class htsjdk.samtools.DefaultSAMRecordFactory.class htsjdk.samtools.Defaults.class htsjdk.samtools.DiskBasedBAMFileIndex.class htsjdk.samtools.DuplicateScoringStrategy.class htsjdk.samtools.FileInputResource.class htsjdk.samtools.FileTruncatedException.class htsjdk.samtools.FixBAMFile.class htsjdk.samtools.GenomicIndexUtil.class htsjdk.samtools.Indexer.class htsjdk.samtools.InputResource.class htsjdk.samtools.InputStreamInputResource.class htsjdk.samtools.LinearIndex.class htsjdk.samtools.MergingSamRecordIterator.class htsjdk.samtools.NotPrimarySkippingIterator.class htsjdk.samtools.QueryInterval.class htsjdk.samtools.ReservedTagConstants.class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue.class htsjdk.samtools.SAMBinaryTagAndValue.class htsjdk.samtools.SAMException.class htsjdk.samtools.SAMFileHeader.class htsjdk.samtools.SAMFileReader.class htsjdk.samtools.SAMFileSource.class htsjdk.samtools.SAMFileSpan.class htsjdk.samtools.SAMFileTruncatedReader.class htsjdk.samtools.SAMFileWriter.class htsjdk.samtools.SAMFileWriterFactory.class htsjdk.samtools.SAMFileWriterImpl.class htsjdk.samtools.SAMFormatException.class htsjdk.samtools.SAMHeaderRecordComparator.class htsjdk.samtools.SAMLineParser.class htsjdk.samtools.SAMProgramRecord.class htsjdk.samtools.SAMReadGroupRecord.class htsjdk.samtools.SAMRecord.class htsjdk.samtools.SAMRecordComparator.class htsjdk.samtools.SAMRecordCoordinateComparator.class htsjdk.samtools.SAMRecordFactory.class htsjdk.samtools.SAMRecordIterator.class htsjdk.samtools.SAMRecordQueryNameComparator.class htsjdk.samtools.SAMRecordSetBuilder.class htsjdk.samtools.SAMRecordUtil.class htsjdk.samtools.SAMSequenceDictionary.class htsjdk.samtools.SAMSequenceRecord.class htsjdk.samtools.SAMSortOrderChecker.class htsjdk.samtools.SAMTag.class htsjdk.samtools.SAMTagUtil.class htsjdk.samtools.SAMTestUtil.class htsjdk.samtools.SAMTextHeaderCodec.class htsjdk.samtools.SAMTextReader.class htsjdk.samtools.SAMTextWriter.class htsjdk.samtools.SAMTools.class htsjdk.samtools.SAMUtils.class htsjdk.samtools.SAMValidationError.class htsjdk.samtools.SQTagUtil.class htsjdk.samtools.SamFileHeaderMerger.class htsjdk.samtools.SamFileValidator.class htsjdk.samtools.SamFiles.class htsjdk.samtools.SamInputResource.class htsjdk.samtools.SamPairUtil.class htsjdk.samtools.SamReader.class htsjdk.samtools.SamReaderFactory.class htsjdk.samtools.SamStreams.class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator.class htsjdk.samtools.SeekableStreamInputResource.class htsjdk.samtools.StreamInflatingIndexingOutputStream.class htsjdk.samtools.TagValueAndUnsignedArrayFlag.class htsjdk.samtools.TextCigarCodec.class htsjdk.samtools.TextTagCodec.class htsjdk.samtools.TextualBAMIndexWriter.class htsjdk.samtools.UrlInputResource.class htsjdk.samtools.ValidationStringency.class htsjdk.samtools.apps.TimeChannel.class htsjdk.samtools.apps.TimeRandomAccessFile.class htsjdk.samtools.cram.build.CompressionHeaderFactory.class htsjdk.samtools.cram.build.ContainerFactory.class htsjdk.samtools.cram.build.ContainerParser.class htsjdk.samtools.cram.build.Cram2SamRecordFactory.class htsjdk.samtools.cram.build.CramBuilder.class htsjdk.samtools.cram.build.CramIO.class htsjdk.samtools.cram.build.CramNormalizer.class htsjdk.samtools.cram.build.Sam2CramRecordFactory.class htsjdk.samtools.cram.build.Utils.class htsjdk.samtools.cram.common.CramVersions.class htsjdk.samtools.cram.common.IntHashMap.class htsjdk.samtools.cram.common.MutableInt.class htsjdk.samtools.cram.common.NonforgivingPrintStream.class htsjdk.samtools.cram.common.NullOutputStream.class htsjdk.samtools.cram.common.Version.class htsjdk.samtools.cram.encoding.AbstractBitCodec.class htsjdk.samtools.cram.encoding.ArithCodec.class htsjdk.samtools.cram.encoding.ArithCodec1.class htsjdk.samtools.cram.encoding.BetaIntegerCodec.class htsjdk.samtools.cram.encoding.BetaIntegerEncoding.class htsjdk.samtools.cram.encoding.BitCodec.class htsjdk.samtools.cram.encoding.ByteArrayLenEncoding.class htsjdk.samtools.cram.encoding.ByteArrayStopEncoding.class htsjdk.samtools.cram.encoding.CanonicalHuffmanByteCodec.class htsjdk.samtools.cram.encoding.CanonicalHuffmanIntegerCodec.class htsjdk.samtools.cram.encoding.DataSeries.class htsjdk.samtools.cram.encoding.DataSeriesMap.class htsjdk.samtools.cram.encoding.DataSeriesType.class htsjdk.samtools.cram.encoding.Encoding.class htsjdk.samtools.cram.encoding.EncodingFactory.class htsjdk.samtools.cram.encoding.ExternalByteArrayCodec.class htsjdk.samtools.cram.encoding.ExternalByteArrayEncoding.class htsjdk.samtools.cram.encoding.ExternalByteCodec.class htsjdk.samtools.cram.encoding.ExternalByteEncoding.class htsjdk.samtools.cram.encoding.ExternalIntegerCodec.class htsjdk.samtools.cram.encoding.ExternalIntegerEncoding.class htsjdk.samtools.cram.encoding.ExternalLongCodec.class htsjdk.samtools.cram.encoding.ExternalLongEncoding.class htsjdk.samtools.cram.encoding.GammaIntegerCodec.class htsjdk.samtools.cram.encoding.GammaIntegerEncoding.class htsjdk.samtools.cram.encoding.GolombIntegerCodec.class htsjdk.samtools.cram.encoding.GolombIntegerEncoding.class htsjdk.samtools.cram.encoding.GolombLongCodec.class htsjdk.samtools.cram.encoding.GolombLongEncoding.class htsjdk.samtools.cram.encoding.GolombRiceIntegerCodec.class htsjdk.samtools.cram.encoding.GolombRiceIntegerEncoding.class htsjdk.samtools.cram.encoding.HuffmanByteEncoding.class htsjdk.samtools.cram.encoding.HuffmanEncoding.class htsjdk.samtools.cram.encoding.HuffmanIntegerEncoding.class htsjdk.samtools.cram.encoding.NullCodec.class htsjdk.samtools.cram.encoding.NullEncoding.class htsjdk.samtools.cram.encoding.SubexpIntegerCodec.class htsjdk.samtools.cram.encoding.SubexpIntegerEncoding.class htsjdk.samtools.cram.encoding.UnaryIntegerCodec.class htsjdk.samtools.cram.encoding.UnaryIntegerEncoding.class htsjdk.samtools.cram.encoding.fastq.Template.class htsjdk.samtools.cram.encoding.huffint.CanonicalHuffmanByteCodec2.class htsjdk.samtools.cram.encoding.huffint.CanonicalHuffmanIntegerCodec2.class htsjdk.samtools.cram.encoding.huffint.Helper.class htsjdk.samtools.cram.encoding.huffint.HelperByte.class htsjdk.samtools.cram.encoding.huffint.HuffmanBitCode.class htsjdk.samtools.cram.encoding.huffint.Node.class htsjdk.samtools.cram.encoding.huffman.HuffmanCode.class htsjdk.samtools.cram.encoding.huffman.HuffmanLeaf.class htsjdk.samtools.cram.encoding.huffman.HuffmanNode.class htsjdk.samtools.cram.encoding.huffman.HuffmanTree.class htsjdk.samtools.cram.encoding.read_features.BaseChange.class htsjdk.samtools.cram.encoding.read_features.BaseQualityScore.class htsjdk.samtools.cram.encoding.read_features.BaseTransitions.class htsjdk.samtools.cram.encoding.read_features.Deletion.class htsjdk.samtools.cram.encoding.read_features.HardClip.class htsjdk.samtools.cram.encoding.read_features.InsertBase.class htsjdk.samtools.cram.encoding.read_features.Insertion.class htsjdk.samtools.cram.encoding.read_features.Padding.class htsjdk.samtools.cram.encoding.read_features.ReadBase.class htsjdk.samtools.cram.encoding.read_features.ReadFeature.class htsjdk.samtools.cram.encoding.read_features.RefSkip.class htsjdk.samtools.cram.encoding.read_features.SoftClip.class htsjdk.samtools.cram.encoding.read_features.Substitution.class htsjdk.samtools.cram.encoding.reader.AbstractFastqReader.class htsjdk.samtools.cram.encoding.reader.AbstractReader.class htsjdk.samtools.cram.encoding.reader.CramRecordReader.class htsjdk.samtools.cram.encoding.reader.DataReader.class htsjdk.samtools.cram.encoding.reader.DataReaderFactory.class htsjdk.samtools.cram.encoding.reader.ReadFeatureBuffer.class htsjdk.samtools.cram.encoding.writer.DataWriter.class htsjdk.samtools.cram.encoding.writer.DataWriterFactory.class htsjdk.samtools.cram.encoding.writer.Writer.class htsjdk.samtools.cram.index.BaiIndexer.class htsjdk.samtools.cram.index.CraiIndexer.class htsjdk.samtools.cram.index.CramIndex.class htsjdk.samtools.cram.io.BitInputStream.class htsjdk.samtools.cram.io.BitOutputStream.class htsjdk.samtools.cram.io.BitwiseUtils.class htsjdk.samtools.cram.io.ByteBufferUtils.class htsjdk.samtools.cram.io.CountingInputStream.class htsjdk.samtools.cram.io.DebuggingInputStream.class htsjdk.samtools.cram.io.DefaultBitInputStream.class htsjdk.samtools.cram.io.DefaultBitOutputStream.class htsjdk.samtools.cram.io.ExposedByteArrayOutputStream.class htsjdk.samtools.cram.lossy.BaseCategory.class htsjdk.samtools.cram.lossy.BaseCategoryType.class htsjdk.samtools.cram.lossy.Binning.class htsjdk.samtools.cram.lossy.PreservationPolicy.class htsjdk.samtools.cram.lossy.QualityScorePreservation.class htsjdk.samtools.cram.lossy.QualityScoreTreatment.class htsjdk.samtools.cram.lossy.QualityScoreTreatmentType.class htsjdk.samtools.cram.lossy.ReadCategory.class htsjdk.samtools.cram.lossy.ReadCategoryType.class htsjdk.samtools.cram.mask.ArrayPositionMask.class htsjdk.samtools.cram.mask.DefaultReadMaskFactory.class htsjdk.samtools.cram.mask.FastaByteArrayMaskFactory.class htsjdk.samtools.cram.mask.IntegerListMaskFactory.class htsjdk.samtools.cram.mask.PositionMask.class htsjdk.samtools.cram.mask.ReadMaskException.class htsjdk.samtools.cram.mask.ReadMaskFactory.class htsjdk.samtools.cram.mask.ReadMaskFormatException.class htsjdk.samtools.cram.mask.ReadMaskReader.class htsjdk.samtools.cram.mask.RefMaskUtils.class htsjdk.samtools.cram.mask.SingleLineMaskReader.class htsjdk.samtools.cram.ref.ReferenceSource.class htsjdk.samtools.cram.ref.ReferenceTracks.class htsjdk.samtools.cram.structure.Block.class htsjdk.samtools.cram.structure.BlockCompressionMethod.class htsjdk.samtools.cram.structure.BlockContentType.class htsjdk.samtools.cram.structure.CompressionHeader.class htsjdk.samtools.cram.structure.CompressionHeaderBLock.class htsjdk.samtools.cram.structure.Container.class htsjdk.samtools.cram.structure.ContainerHeaderIO.class htsjdk.samtools.cram.structure.CramCompressionRecord.class htsjdk.samtools.cram.structure.CramHeader.class htsjdk.samtools.cram.structure.EncodingID.class htsjdk.samtools.cram.structure.EncodingKey.class htsjdk.samtools.cram.structure.EncodingParams.class htsjdk.samtools.cram.structure.ReadTag.class htsjdk.samtools.cram.structure.Slice.class htsjdk.samtools.cram.structure.SliceHeader.class htsjdk.samtools.cram.structure.SliceIO.class htsjdk.samtools.cram.structure.SubstitutionMatrix.class htsjdk.samtools.example.ExampleSamUsage.class htsjdk.samtools.fastq.AsyncFastqWriter.class htsjdk.samtools.fastq.BasicFastqWriter.class htsjdk.samtools.fastq.FastqConstants.class htsjdk.samtools.fastq.FastqReader.class htsjdk.samtools.fastq.FastqRecord.class htsjdk.samtools.fastq.FastqWriter.class htsjdk.samtools.fastq.FastqWriterFactory.class htsjdk.samtools.filter.AggregateFilter.class htsjdk.samtools.filter.AlignedFilter.class htsjdk.samtools.filter.DuplicateReadFilter.class htsjdk.samtools.filter.FailsVendorReadQualityFilter.class htsjdk.samtools.filter.FilteringIterator.class htsjdk.samtools.filter.IntervalFilter.class htsjdk.samtools.filter.NotPrimaryAlignmentFilter.class htsjdk.samtools.filter.ReadNameFilter.class htsjdk.samtools.filter.SamRecordFilter.class htsjdk.samtools.filter.SecondaryAlignmentFilter.class htsjdk.samtools.filter.SecondaryOrSupplementaryFilter.class htsjdk.samtools.filter.SolexaNoiseFilter.class htsjdk.samtools.filter.TagFilter.class htsjdk.samtools.filter.WholeReadClippedFilter.class htsjdk.samtools.liftover.Chain.class htsjdk.samtools.liftover.LiftOver.class htsjdk.samtools.metrics.Header.class htsjdk.samtools.metrics.MetricBase.class htsjdk.samtools.metrics.MetricsFile.class htsjdk.samtools.metrics.StringHeader.class htsjdk.samtools.metrics.VersionHeader.class htsjdk.samtools.reference.AbstractFastaSequenceFile.class htsjdk.samtools.reference.FastaSequenceFile.class htsjdk.samtools.reference.FastaSequenceIndex.class htsjdk.samtools.reference.FastaSequenceIndexEntry.class htsjdk.samtools.reference.IndexedFastaSequenceFile.class htsjdk.samtools.reference.ReferenceSequence.class htsjdk.samtools.reference.ReferenceSequenceFile.class htsjdk.samtools.reference.ReferenceSequenceFileFactory.class htsjdk.samtools.reference.ReferenceSequenceFileWalker.class htsjdk.samtools.seekablestream.ISeekableStreamFactory.class htsjdk.samtools.seekablestream.SeekableBufferedStream.class htsjdk.samtools.seekablestream.SeekableFTPStream.class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper.class htsjdk.samtools.seekablestream.SeekableFileStream.class htsjdk.samtools.seekablestream.SeekableHTTPStream.class htsjdk.samtools.seekablestream.SeekableStream.class htsjdk.samtools.seekablestream.SeekableStreamFactory.class htsjdk.samtools.seekablestream.UserPasswordInput.class htsjdk.samtools.util.AbstractAsyncWriter.class htsjdk.samtools.util.AbstractIterator.class htsjdk.samtools.util.AsciiWriter.class htsjdk.samtools.util.BinaryCodec.class htsjdk.samtools.util.BlockCompressedFilePointerUtil.class htsjdk.samtools.util.BlockCompressedInputStream.class htsjdk.samtools.util.BlockCompressedOutputStream.class htsjdk.samtools.util.BlockCompressedStreamConstants.class htsjdk.samtools.util.BlockGunzipper.class htsjdk.samtools.util.BufferedLineReader.class htsjdk.samtools.util.CigarUtil.class htsjdk.samtools.util.CloseableIterator.class htsjdk.samtools.util.CloserUtil.class htsjdk.samtools.util.CollectionUtil.class htsjdk.samtools.util.CoordMath.class htsjdk.samtools.util.CustomGzipOutputStream.class htsjdk.samtools.util.DateParser.class htsjdk.samtools.util.DelegatingIterator.class htsjdk.samtools.util.DiskBackedQueue.class htsjdk.samtools.util.FastLineReader.class htsjdk.samtools.util.FastqQualityFormat.class htsjdk.samtools.util.FileAppendStreamLRUCache.class htsjdk.samtools.util.FormatUtil.class htsjdk.samtools.util.Histogram.class htsjdk.samtools.util.HttpUtils.class htsjdk.samtools.util.IOUtil.class htsjdk.samtools.util.Interval.class htsjdk.samtools.util.IntervalCoordinateComparator.class htsjdk.samtools.util.IntervalList.class htsjdk.samtools.util.IntervalListReferenceSequenceMask.class htsjdk.samtools.util.IntervalTree.class htsjdk.samtools.util.IntervalTreeMap.class htsjdk.samtools.util.IntervalUtil.class htsjdk.samtools.util.Iso8601Date.class htsjdk.samtools.util.IterableAdapter.class htsjdk.samtools.util.IterableOnceIterator.class htsjdk.samtools.util.Iterables.class htsjdk.samtools.util.Lazy.class htsjdk.samtools.util.LineReader.class htsjdk.samtools.util.ListMap.class htsjdk.samtools.util.LocationAware.class htsjdk.samtools.util.Locus.class htsjdk.samtools.util.LocusComparator.class htsjdk.samtools.util.LocusImpl.class htsjdk.samtools.util.Log.class htsjdk.samtools.util.Md5CalculatingInputStream.class htsjdk.samtools.util.Md5CalculatingOutputStream.class htsjdk.samtools.util.MergingIterator.class htsjdk.samtools.util.Objects.class htsjdk.samtools.util.OverlapDetector.class htsjdk.samtools.util.PeekIterator.class htsjdk.samtools.util.PeekableIterator.class htsjdk.samtools.util.ProcessExecutor.class htsjdk.samtools.util.ProgressLogger.class htsjdk.samtools.util.ProgressLoggerInterface.class htsjdk.samtools.util.QualityEncodingDetector.class htsjdk.samtools.util.QualityUtil.class htsjdk.samtools.util.ReferenceSequenceMask.class htsjdk.samtools.util.RelativeIso8601Date.class htsjdk.samtools.util.ResourceLimitedMap.class htsjdk.samtools.util.ResourceLimitedMapFunctor.class htsjdk.samtools.util.RuntimeEOFException.class htsjdk.samtools.util.RuntimeIOException.class htsjdk.samtools.util.SamLocusIterator.class htsjdk.samtools.util.SamRecordIntervalIteratorFactory.class htsjdk.samtools.util.SamRecordTrackingBuffer.class htsjdk.samtools.util.SamRecordWithOrdinal.class htsjdk.samtools.util.SequenceUtil.class htsjdk.samtools.util.SnappyLoader.class htsjdk.samtools.util.SolexaQualityConverter.class htsjdk.samtools.util.SortingCollection.class htsjdk.samtools.util.SortingLongCollection.class htsjdk.samtools.util.StopWatch.class htsjdk.samtools.util.StringLineReader.class htsjdk.samtools.util.StringUtil.class htsjdk.samtools.util.TempStreamFactory.class htsjdk.samtools.util.TestUtil.class htsjdk.samtools.util.Tuple.class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask.class htsjdk.samtools.util.ftp.FTPClient.class htsjdk.samtools.util.ftp.FTPReply.class htsjdk.samtools.util.ftp.FTPStream.class htsjdk.samtools.util.ftp.FTPUtils.class htsjdk.samtools.util.zip.DeflaterFactory.class htsjdk.samtools.util.zip.IntelDeflater.class htsjdk.samtools.util.zip.ZStreamRef.class htsjdk.tribble.AbstractFeatureCodec.class htsjdk.tribble.AbstractFeatureReader.class htsjdk.tribble.AsciiFeatureCodec.class htsjdk.tribble.BasicFeature.class htsjdk.tribble.BinaryFeatureCodec.class htsjdk.tribble.CloseableTribbleIterator.class htsjdk.tribble.Feature.class htsjdk.tribble.FeatureCodec.class htsjdk.tribble.FeatureCodecHeader.class htsjdk.tribble.FeatureReader.class htsjdk.tribble.NameAwareCodec.class htsjdk.tribble.TabixFeatureReader.class htsjdk.tribble.Tribble.class htsjdk.tribble.TribbleException.class htsjdk.tribble.TribbleIndexedFeatureReader.class htsjdk.tribble.annotation.Strand.class htsjdk.tribble.bed.BEDCodec.class htsjdk.tribble.bed.BEDFeature.class htsjdk.tribble.bed.FullBEDFeature.class htsjdk.tribble.bed.SimpleBEDFeature.class htsjdk.tribble.dbsnp.OldDbSNPCodec.class htsjdk.tribble.dbsnp.OldDbSNPFeature.class htsjdk.tribble.example.CountRecords.class htsjdk.tribble.example.ExampleBinaryCodec.class htsjdk.tribble.example.IndexToTable.class htsjdk.tribble.example.IndicesAreEqual.class htsjdk.tribble.example.ProfileIndexReading.class htsjdk.tribble.exception.CodecLineParsingException.class htsjdk.tribble.exception.UnsortedFileException.class htsjdk.tribble.gelitext.DiploidGenotype.class htsjdk.tribble.gelitext.DiploidGenotypeException.class htsjdk.tribble.gelitext.GeliTextCodec.class htsjdk.tribble.gelitext.GeliTextFeature.class htsjdk.tribble.index.AbstractIndex.class htsjdk.tribble.index.Block.class htsjdk.tribble.index.ChrIndex.class htsjdk.tribble.index.DynamicIndexCreator.class htsjdk.tribble.index.Index.class htsjdk.tribble.index.IndexCreator.class htsjdk.tribble.index.IndexFactory.class htsjdk.tribble.index.MutableIndex.class htsjdk.tribble.index.TribbleIndexCreator.class htsjdk.tribble.index.interval.Interval.class htsjdk.tribble.index.interval.IntervalIndexCreator.class htsjdk.tribble.index.interval.IntervalTree.class htsjdk.tribble.index.interval.IntervalTreeIndex.class htsjdk.tribble.index.interval.MutableInterval.class htsjdk.tribble.index.linear.LinearIndex.class htsjdk.tribble.index.linear.LinearIndexCreator.class htsjdk.tribble.index.tabix.TabixFormat.class htsjdk.tribble.index.tabix.TabixIndex.class htsjdk.tribble.index.tabix.TabixIndexCreator.class htsjdk.tribble.readers.AsciiLineReader.class htsjdk.tribble.readers.AsciiLineReaderIterator.class htsjdk.tribble.readers.AsynchronousLineReader.class htsjdk.tribble.readers.LineIterator.class htsjdk.tribble.readers.LineIteratorImpl.class htsjdk.tribble.readers.LineReader.class htsjdk.tribble.readers.LineReaderUtil.class htsjdk.tribble.readers.LongLineBufferedReader.class htsjdk.tribble.readers.Positional.class htsjdk.tribble.readers.PositionalBufferedStream.class htsjdk.tribble.readers.TabixIteratorLineReader.class htsjdk.tribble.readers.TabixReader.class htsjdk.tribble.util.FTPHelper.class htsjdk.tribble.util.HTTPHelper.class htsjdk.tribble.util.LittleEndianInputStream.class htsjdk.tribble.util.LittleEndianOutputStream.class htsjdk.tribble.util.MathUtils.class htsjdk.tribble.util.ParsingUtils.class htsjdk.tribble.util.RemoteURLHelper.class htsjdk.tribble.util.TabixUtils.class htsjdk.tribble.util.URLHelper.class htsjdk.tribble.util.popgen.HardyWeinbergCalculation.class htsjdk.variant.bcf2.BCF2Codec.class htsjdk.variant.bcf2.BCF2Decoder.class htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders.class htsjdk.variant.bcf2.BCF2LazyGenotypesDecoder.class htsjdk.variant.bcf2.BCF2Type.class htsjdk.variant.bcf2.BCF2Utils.class htsjdk.variant.bcf2.BCFVersion.class htsjdk.variant.utils.GeneralUtils.class htsjdk.variant.utils.SAMSequenceDictionaryExtractor.class htsjdk.variant.variantcontext.Allele.class htsjdk.variant.variantcontext.CommonInfo.class htsjdk.variant.variantcontext.FastGenotype.class htsjdk.variant.variantcontext.Genotype.class htsjdk.variant.variantcontext.GenotypeBuilder.class htsjdk.variant.variantcontext.GenotypeLikelihoods.class htsjdk.variant.variantcontext.GenotypeType.class htsjdk.variant.variantcontext.GenotypesContext.class htsjdk.variant.variantcontext.JEXLMap.class htsjdk.variant.variantcontext.LazyGenotypesContext.class htsjdk.variant.variantcontext.VariantContext.class htsjdk.variant.variantcontext.VariantContextBuilder.class htsjdk.variant.variantcontext.VariantContextComparator.class htsjdk.variant.variantcontext.VariantContextUtils.class htsjdk.variant.variantcontext.VariantJEXLContext.class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter.class htsjdk.variant.variantcontext.writer.BCF2Encoder.class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager.class htsjdk.variant.variantcontext.writer.BCF2Writer.class htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.class htsjdk.variant.variantcontext.writer.Options.class htsjdk.variant.variantcontext.writer.PositionalOutputStream.class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter.class htsjdk.variant.variantcontext.writer.SortingVariantContextWriterBase.class htsjdk.variant.variantcontext.writer.VCFWriter.class htsjdk.variant.variantcontext.writer.VariantContextWriter.class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory.class htsjdk.variant.vcf.AbstractVCFCodec.class htsjdk.variant.vcf.VCF3Codec.class htsjdk.variant.vcf.VCF3Parser.class htsjdk.variant.vcf.VCF4Parser.class htsjdk.variant.vcf.VCFCodec.class htsjdk.variant.vcf.VCFCompoundHeaderLine.class htsjdk.variant.vcf.VCFConstants.class htsjdk.variant.vcf.VCFContigHeaderLine.class htsjdk.variant.vcf.VCFEncoder.class htsjdk.variant.vcf.VCFFileReader.class htsjdk.variant.vcf.VCFFilterHeaderLine.class htsjdk.variant.vcf.VCFFormatHeaderLine.class htsjdk.variant.vcf.VCFHeader.class htsjdk.variant.vcf.VCFHeaderLine.class htsjdk.variant.vcf.VCFHeaderLineCount.class htsjdk.variant.vcf.VCFHeaderLineTranslator.class htsjdk.variant.vcf.VCFHeaderLineType.class htsjdk.variant.vcf.VCFHeaderVersion.class htsjdk.variant.vcf.VCFIDHeaderLine.class htsjdk.variant.vcf.VCFInfoHeaderLine.class htsjdk.variant.vcf.VCFLineParser.class htsjdk.variant.vcf.VCFRecordCodec.class htsjdk.variant.vcf.VCFSimpleHeaderLine.class htsjdk.variant.vcf.VCFStandardHeaderLines.class htsjdk.variant.vcf.VCFUtils.class
htsjdk-1.128.pom file content.
<?xml version='1.0' encoding='UTF-8'?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0">
<modelVersion>4.0.0</modelVersion>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<packaging>jar</packaging>
<description>htsjdk</description>
<version>1.128</version>
<name>htsjdk</name>
<organization>
<name>com.github.samtools</name>
</organization>
<url>http://samtools.github.io/htsjdk/</url>
<licenses>
<license>
<name>MIT License</name>
<url>http://opensource.org/licenses/MIT</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<url>git@github.com:samtools/htsjdk.git</url>
<connection>scm:git:git@github.com:samtools/htsjdk.git</connection>
</scm>
<developers>
<developer>
<id>picard</id>
<name>Picard Team</name>
<url>http://broadinstitute.github.io/picard/</url>
</developer>
</developers>
<dependencies>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.11.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-jexl</artifactId>
<version>2.1.1</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>org.xerial.snappy</groupId>
<artifactId>snappy-java</artifactId>
<version>1.1.1.3</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8.8</version>
</dependency>
<dependency>
<groupId>org.yaml</groupId>
<artifactId>snakeyaml</artifactId>
<version>1.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>de.johoop</groupId>
<artifactId>sbt-testng-interface_2.11</artifactId>
<version>3.0.2</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
<dependency> <groupId>com.github.samtools</groupId> <artifactId>htsjdk</artifactId> <version>1.128</version> </dependency>
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Download htsjdk-1.128.jar file