Hierarchy For All Packages

Package Hierarchies:

htsjdk.samtools, htsjdk.samtools.apps, htsjdk.samtools.cram.build, htsjdk.samtools.cram.common, htsjdk.samtools.cram.encoding, htsjdk.samtools.cram.encoding.fastq, htsjdk.samtools.cram.encoding.huffint, htsjdk.samtools.cram.encoding.huffman, htsjdk.samtools.cram.encoding.read_features, htsjdk.samtools.cram.encoding.reader, htsjdk.samtools.cram.encoding.writer, htsjdk.samtools.cram.index, htsjdk.samtools.cram.io, htsjdk.samtools.cram.lossy, htsjdk.samtools.cram.mask, htsjdk.samtools.cram.ref, htsjdk.samtools.cram.structure, htsjdk.samtools.example, htsjdk.samtools.fastq, htsjdk.samtools.filter, htsjdk.samtools.liftover, htsjdk.samtools.metrics, htsjdk.samtools.reference, htsjdk.samtools.seekablestream, htsjdk.samtools.util, htsjdk.samtools.util.ftp, htsjdk.samtools.util.zip, htsjdk.tribble, htsjdk.tribble.annotation, htsjdk.tribble.bed, htsjdk.tribble.dbsnp, htsjdk.tribble.example, htsjdk.tribble.exception, htsjdk.tribble.gelitext, htsjdk.tribble.index, htsjdk.tribble.index.interval, htsjdk.tribble.index.linear, htsjdk.tribble.index.tabix, htsjdk.tribble.readers, htsjdk.tribble.util, htsjdk.tribble.util.popgen, htsjdk.variant.bcf2, htsjdk.variant.utils, htsjdk.variant.variantcontext, htsjdk.variant.variantcontext.writer, htsjdk.variant.vcf

Class Hierarchy

• java.lang.Object
  • htsjdk.samtools.util.AbstractAsyncWriter<T> (implements java.io.Closeable)
    • htsjdk.samtools.fastq.AsyncFastqWriter (implements htsjdk.samtools.fastq.FastqWriter)
    • htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter (implements htsjdk.variant.variantcontext.writer.VariantContextWriter)
  • htsjdk.samtools.AbstractBAMFileIndex (implements htsjdk.samtools.BAMIndex)
  • htsjdk.samtools.cram.encoding.AbstractBitCodec<T> (implements htsjdk.samtools.cram.encoding.BitCodec<T>)
    • htsjdk.samtools.cram.encoding.ArithCodec
    • htsjdk.samtools.cram.encoding.ArithCodec1
    • htsjdk.samtools.cram.encoding.BetaIntegerCodec
    • htsjdk.samtools.cram.encoding.ByteArrayStopEncoding.ByteArrayStopCodec
    • htsjdk.samtools.cram.encoding.CanonicalHuffmanByteCodec
    • htsjdk.samtools.cram.encoding.huffint.CanonicalHuffmanByteCodec2
    • htsjdk.samtools.cram.encoding.CanonicalHuffmanIntegerCodec
    • htsjdk.samtools.cram.encoding.huffint.CanonicalHuffmanIntegerCodec2
    • htsjdk.samtools.cram.encoding.ExternalByteArrayCodec
    • htsjdk.samtools.cram.encoding.ExternalByteCodec
    • htsjdk.samtools.cram.encoding.ExternalIntegerCodec
    • htsjdk.samtools.cram.encoding.ExternalLongCodec
    • htsjdk.samtools.cram.encoding.GammaIntegerCodec
    • htsjdk.samtools.cram.encoding.GolombIntegerCodec
    • htsjdk.samtools.cram.encoding.GolombLongCodec
    • htsjdk.samtools.cram.encoding.GolombRiceIntegerCodec
    • htsjdk.samtools.cram.encoding.NullCodec<T>
    • htsjdk.samtools.cram.encoding.SubexpIntegerCodec
    • htsjdk.samtools.cram.encoding.UnaryIntegerCodec
  • htsjdk.tribble.AbstractFeatureCodec<FEATURE_TYPE,SOURCE> (implements htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>)
    • htsjdk.tribble.AsciiFeatureCodec<T>
      • htsjdk.variant.vcf.AbstractVCFCodec (implements htsjdk.tribble.NameAwareCodec)
        • htsjdk.variant.vcf.VCF3Codec
        • htsjdk.variant.vcf.VCFCodec
      • htsjdk.tribble.bed.BEDCodec
      • htsjdk.tribble.gelitext.GeliTextCodec
      • htsjdk.tribble.dbsnp.OldDbSNPCodec
  • htsjdk.tribble.AbstractFeatureReader<T,SOURCE> (implements htsjdk.tribble.FeatureReader<T>)
    • htsjdk.tribble.TabixFeatureReader<T,SOURCE>
    • htsjdk.tribble.TribbleIndexedFeatureReader<T,SOURCE>
  • htsjdk.tribble.AbstractFeatureReader.ComponentMethods
  • htsjdk.tribble.index.AbstractIndex (implements htsjdk.tribble.index.MutableIndex)
    • htsjdk.tribble.index.interval.IntervalTreeIndex
    • htsjdk.tribble.index.linear.LinearIndex
  • htsjdk.tribble.index.AbstractIndex.BlockStats
  • htsjdk.samtools.util.AbstractIterator<E> (implements java.util.Iterator<E>)
    • htsjdk.tribble.readers.LineIteratorImpl (implements java.io.Closeable, htsjdk.tribble.readers.LineIterator)
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • htsjdk.samtools.util.CollectionUtil.DefaultingMap<K,V>
      • htsjdk.samtools.util.CollectionUtil.MultiMap<K,V>
      • htsjdk.samtools.util.ListMap<K,V>
    • htsjdk.samtools.util.IntervalTreeMap<T>
    • java.util.TreeMap<K,V> (implements java.lang.Cloneable, java.util.NavigableMap<K,V>, java.io.Serializable)
      • htsjdk.samtools.util.Histogram<K>
  • htsjdk.samtools.cram.encoding.reader.AbstractReader
    • htsjdk.samtools.cram.encoding.reader.AbstractFastqReader
    • htsjdk.samtools.cram.encoding.reader.CramRecordReader
  • htsjdk.samtools.AbstractSAMHeaderRecord
    • htsjdk.samtools.SAMFileHeader
    • htsjdk.samtools.SAMProgramRecord
    • htsjdk.samtools.SAMReadGroupRecord
    • htsjdk.samtools.SAMSequenceRecord (implements java.lang.Cloneable)
  • htsjdk.samtools.filter.AggregateFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.filter.AlignedFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.AlignmentBlock
  • htsjdk.variant.variantcontext.Allele (implements java.lang.Comparable<T>)
  • htsjdk.samtools.cram.mask.ArrayPositionMask (implements htsjdk.samtools.cram.mask.PositionMask)
  • htsjdk.tribble.readers.AsciiLineReader (implements htsjdk.tribble.readers.LineReader, htsjdk.samtools.util.LocationAware)
  • htsjdk.tribble.readers.AsciiLineReaderIterator (implements java.io.Closeable, htsjdk.tribble.readers.LineIterator, htsjdk.samtools.util.LocationAware)
  • htsjdk.tribble.readers.AsynchronousLineReader (implements htsjdk.tribble.readers.LineReader)
  • htsjdk.samtools.BamFileIoUtils
  • htsjdk.samtools.BAMIndexer
  • htsjdk.samtools.BAMIndexMetaData
  • htsjdk.samtools.BamIndexValidator
  • htsjdk.samtools.BAMRecordCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
  • htsjdk.samtools.cram.lossy.BaseCategory
  • htsjdk.samtools.cram.encoding.read_features.BaseChange (implements java.io.Serializable)
  • htsjdk.samtools.cram.encoding.read_features.BaseQualityScore (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.samtools.fastq.BasicFastqWriter (implements htsjdk.samtools.fastq.FastqWriter)
  • htsjdk.tribble.BasicFeature (implements htsjdk.tribble.Feature)
  • htsjdk.variant.bcf2.BCF2Codec.LazyData
  • htsjdk.variant.bcf2.BCF2Codec.SitesInfoForDecoding
  • htsjdk.variant.bcf2.BCF2Decoder
  • htsjdk.variant.variantcontext.writer.BCF2Encoder
  • htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
    • htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.AtomicInt
    • htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Flag
    • htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.Float
    • htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.GenericInts
    • htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.IntArray
    • htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.StringOrCharacter
  • htsjdk.variant.variantcontext.writer.BCF2FieldWriter
    • htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenotypesWriter
      • htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GTWriter
      • htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IGFGenotypesWriter
      • htsjdk.variant.variantcontext.writer.BCF2FieldWriter.IntegerTypeGenotypesWriter
      • htsjdk.variant.variantcontext.writer.BCF2FieldWriter.StaticallyTypeGenotypesWriter
        • htsjdk.variant.variantcontext.writer.BCF2FieldWriter.FTGenotypesWriter
    • htsjdk.variant.variantcontext.writer.BCF2FieldWriter.SiteWriter
      • htsjdk.variant.variantcontext.writer.BCF2FieldWriter.GenericSiteWriter
  • htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager
  • htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders
  • htsjdk.variant.bcf2.BCF2LazyGenotypesDecoder (implements htsjdk.variant.variantcontext.LazyGenotypesContext.LazyParser)
  • htsjdk.variant.bcf2.BCF2Utils
  • htsjdk.variant.bcf2.BCFVersion
  • htsjdk.samtools.cram.encoding.BetaIntegerEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.Bin (implements java.lang.Comparable<T>)
  • htsjdk.samtools.util.BinaryCodec (implements java.io.Closeable)
  • htsjdk.tribble.BinaryFeatureCodec<T> (implements htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>)
    • htsjdk.variant.bcf2.BCF2Codec
    • htsjdk.tribble.example.ExampleBinaryCodec
  • htsjdk.samtools.BinList (implements java.lang.Iterable<T>)
  • htsjdk.samtools.cram.lossy.Binning
  • htsjdk.samtools.BinningIndexBuilder
  • htsjdk.samtools.BinningIndexContent
  • htsjdk.samtools.BinningIndexContent.BinList (implements java.lang.Iterable<T>)
  • htsjdk.samtools.cram.io.BitwiseUtils
  • htsjdk.samtools.cram.structure.Block
    • htsjdk.samtools.cram.structure.CompressionHeaderBLock
  • htsjdk.tribble.index.Block
  • htsjdk.samtools.util.BlockCompressedFilePointerUtil
  • htsjdk.samtools.util.BlockCompressedStreamConstants
  • htsjdk.samtools.util.BlockGunzipper
  • htsjdk.samtools.util.BufferedLineReader (implements htsjdk.samtools.util.LineReader)
  • htsjdk.samtools.cram.encoding.ByteArrayLenEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.ByteArrayStopEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.io.ByteBufferUtils
  • htsjdk.samtools.Chunk (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
  • htsjdk.samtools.Cigar
  • htsjdk.samtools.CigarElement
  • htsjdk.samtools.util.CigarUtil
  • htsjdk.samtools.util.CloserUtil
  • htsjdk.samtools.util.CollectionUtil
  • htsjdk.samtools.util.CollectionUtil.Partitioner<V,K>
  • htsjdk.variant.variantcontext.CommonInfo
  • htsjdk.samtools.cram.structure.CompressionHeader
  • htsjdk.samtools.cram.build.CompressionHeaderFactory
  • htsjdk.samtools.cram.build.CompressionHeaderFactory.EncodingLengthCalculator
  • htsjdk.samtools.cram.build.CompressionHeaderFactory.HuffmanParamsCalculator
  • htsjdk.samtools.cram.build.CompressionHeaderFactory.IntegerEncodingCalculator
  • htsjdk.samtools.cram.structure.Container
  • htsjdk.samtools.cram.build.ContainerFactory
  • htsjdk.samtools.cram.structure.ContainerHeaderIO
  • htsjdk.samtools.cram.build.ContainerParser
  • htsjdk.samtools.CoordinateSortedPairInfoMap<KEY,REC> (implements java.lang.Iterable<T>)
  • htsjdk.samtools.util.CoordMath
  • htsjdk.tribble.example.CountRecords
  • htsjdk.samtools.cram.build.Cram2SamRecordFactory
  • htsjdk.samtools.cram.build.CramBuilder
  • htsjdk.samtools.cram.structure.CramCompressionRecord
  • htsjdk.samtools.cram.structure.CramCompressionRecord.BAM_FLAGS
  • htsjdk.samtools.cram.structure.CramHeader
  • htsjdk.samtools.cram.index.CramIndex
  • htsjdk.samtools.cram.index.CramIndex.Entry (implements java.lang.Cloneable, java.lang.Comparable<T>)
  • htsjdk.samtools.CRAMIndexer
  • htsjdk.samtools.cram.build.CramIO
  • htsjdk.samtools.CRAMIterator (implements htsjdk.samtools.SAMRecordIterator)
  • htsjdk.samtools.CRAMIterator.CramFileIterable (implements java.lang.Iterable<T>)
  • htsjdk.samtools.cram.build.CramNormalizer
  • htsjdk.samtools.cram.common.CramVersions
  • htsjdk.samtools.CustomReaderFactory
  • htsjdk.samtools.cram.encoding.reader.DataReaderFactory
  • htsjdk.samtools.cram.encoding.reader.DataReaderFactory.DataReaderWithStats<T> (implements htsjdk.samtools.cram.encoding.reader.DataReader<T>)
  • htsjdk.samtools.cram.encoding.writer.DataWriterFactory
  • java.util.Date (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
    • htsjdk.samtools.util.Iso8601Date
      • htsjdk.samtools.util.RelativeIso8601Date
  • htsjdk.samtools.util.DateParser
  • htsjdk.samtools.cram.mask.DefaultReadMaskFactory (implements htsjdk.samtools.cram.mask.ReadMaskFactory<T>)
  • htsjdk.samtools.Defaults
  • htsjdk.samtools.DefaultSAMRecordFactory (implements htsjdk.samtools.SAMRecordFactory)
  • java.util.zip.Deflater
    • htsjdk.samtools.util.zip.IntelDeflater
  • htsjdk.samtools.util.zip.DeflaterFactory
  • htsjdk.samtools.util.DelegatingIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
  • htsjdk.samtools.cram.encoding.read_features.Deletion (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.samtools.util.DiskBackedQueue<E> (implements java.util.Queue<E>)
  • htsjdk.samtools.filter.DuplicateReadFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.DuplicateScoringStrategy
  • htsjdk.samtools.cram.encoding.EncodingFactory
  • htsjdk.samtools.cram.structure.EncodingParams
  • htsjdk.samtools.example.ExampleSamUsage
  • htsjdk.samtools.cram.encoding.ExternalByteArrayEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.ExternalByteEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.ExternalIntegerEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.ExternalLongEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.filter.FailsVendorReadQualityFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.cram.mask.FastaByteArrayMaskFactory (implements htsjdk.samtools.cram.mask.ReadMaskFactory<T>)
  • htsjdk.samtools.reference.FastaSequenceFile
  • htsjdk.samtools.reference.FastaSequenceIndex (implements java.lang.Iterable<T>)
  • htsjdk.samtools.util.FastLineReader (implements java.io.Closeable)
  • htsjdk.samtools.fastq.FastqConstants
  • htsjdk.samtools.fastq.FastqReader (implements java.io.Closeable, java.lang.Iterable<T>, java.util.Iterator<E>)
  • htsjdk.samtools.fastq.FastqRecord
  • htsjdk.samtools.fastq.FastqWriterFactory
  • htsjdk.tribble.FeatureCodecHeader
  • htsjdk.samtools.filter.FilteringIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
  • htsjdk.samtools.FixBAMFile
  • htsjdk.samtools.util.FormatUtil
  • htsjdk.samtools.util.ftp.FTPClient
  • htsjdk.tribble.util.FTPHelper (implements htsjdk.tribble.util.URLHelper)
  • htsjdk.samtools.util.ftp.FTPReply
  • htsjdk.samtools.util.ftp.FTPUtils
  • htsjdk.tribble.bed.FullBEDFeature.Exon
  • htsjdk.tribble.bed.FullBEDFeature.Exon2
  • htsjdk.samtools.cram.encoding.GammaIntegerEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.tribble.gelitext.GeliTextFeature (implements htsjdk.tribble.Feature)
  • htsjdk.variant.utils.GeneralUtils
  • htsjdk.samtools.GenomicIndexUtil
  • htsjdk.variant.variantcontext.Genotype (implements java.lang.Comparable<T>)
    • htsjdk.variant.variantcontext.FastGenotype
  • htsjdk.variant.variantcontext.GenotypeBuilder
  • htsjdk.variant.variantcontext.GenotypeLikelihoods
  • htsjdk.variant.variantcontext.GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
  • htsjdk.variant.variantcontext.GenotypesContext (implements java.util.List<E>)
    • htsjdk.variant.variantcontext.LazyGenotypesContext
  • htsjdk.samtools.cram.encoding.GolombIntegerEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.GolombLongEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.GolombRiceIntegerEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.read_features.HardClip (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.tribble.util.popgen.HardyWeinbergCalculation
  • htsjdk.samtools.util.Histogram.Bin
  • htsjdk.tribble.util.HTTPHelper (implements htsjdk.tribble.util.URLHelper)
  • htsjdk.samtools.util.HttpUtils
  • htsjdk.samtools.cram.encoding.HuffmanByteEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.huffman.HuffmanCode
  • htsjdk.samtools.cram.encoding.HuffmanEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.HuffmanIntegerEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.huffman.HuffmanTree<T> (implements java.lang.Comparable<T>)
    • htsjdk.samtools.cram.encoding.huffman.HuffmanLeaf<T>
    • htsjdk.samtools.cram.encoding.huffman.HuffmanNode<T>
  • htsjdk.samtools.reference.IndexedFastaSequenceFile (implements java.io.Closeable)
  • htsjdk.tribble.index.IndexFactory
  • htsjdk.tribble.example.IndexToTable
  • htsjdk.tribble.example.IndicesAreEqual
  • java.io.InputStream (implements java.io.Closeable)
    • htsjdk.samtools.util.BlockCompressedInputStream (implements htsjdk.samtools.util.LocationAware)
    • htsjdk.samtools.cram.io.CountingInputStream
    • htsjdk.samtools.cram.io.DebuggingInputStream
    • java.io.FilterInputStream
      • java.io.DataInputStream (implements java.io.DataInput)
        • htsjdk.samtools.cram.io.DefaultBitInputStream (implements htsjdk.samtools.cram.io.BitInputStream)
      • htsjdk.samtools.util.ftp.FTPStream
      • htsjdk.tribble.util.LittleEndianInputStream
    • htsjdk.samtools.util.Md5CalculatingInputStream
    • htsjdk.tribble.readers.PositionalBufferedStream (implements htsjdk.tribble.readers.Positional)
    • htsjdk.samtools.seekablestream.SeekableStream
      • htsjdk.samtools.seekablestream.SeekableBufferedStream
      • htsjdk.samtools.seekablestream.SeekableFileStream
      • htsjdk.samtools.seekablestream.SeekableFTPStream
      • htsjdk.samtools.seekablestream.SeekableHTTPStream
  • htsjdk.samtools.cram.encoding.read_features.InsertBase (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.samtools.cram.encoding.read_features.Insertion (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.samtools.cram.mask.IntegerListMaskFactory (implements htsjdk.samtools.cram.mask.ReadMaskFactory<T>)
  • htsjdk.samtools.util.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>)
  • htsjdk.tribble.index.interval.Interval (implements java.lang.Comparable<T>)
  • htsjdk.samtools.filter.IntervalFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.util.IntervalList (implements java.lang.Iterable<T>)
  • htsjdk.samtools.util.IntervalListReferenceSequenceMask (implements htsjdk.samtools.util.ReferenceSequenceMask)
  • htsjdk.samtools.util.IntervalTree<V> (implements java.lang.Iterable<T>)
  • htsjdk.tribble.index.interval.IntervalTree
  • htsjdk.samtools.util.IntervalTree.FwdIterator (implements java.util.Iterator<E>)
  • htsjdk.samtools.util.IntervalTree.Node<V1>
  • htsjdk.samtools.util.IntervalTree.OverlapIterator (implements java.util.Iterator<E>)
  • htsjdk.samtools.util.IntervalTree.RevIterator (implements java.util.Iterator<E>)
  • htsjdk.samtools.util.IntervalTree.ValuesIterator<V1> (implements java.util.Iterator<E>)
  • htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex (implements htsjdk.tribble.index.ChrIndex)
  • htsjdk.samtools.util.IntervalUtil
  • htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors
  • htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.Accessor
    • htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.ADAccessor
    • htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.DPAccessor
    • htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.GQAccessor
    • htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.PLAccessor
  • htsjdk.samtools.cram.common.IntHashMap<T>
  • htsjdk.samtools.util.IOUtil
  • htsjdk.samtools.util.IterableAdapter<T> (implements java.lang.Iterable<T>)
  • htsjdk.samtools.util.IterableOnceIterator<T> (implements java.io.Closeable, java.lang.Iterable<T>, java.util.Iterator<E>)
  • htsjdk.samtools.util.Iterables
  • htsjdk.samtools.util.Lazy<T>
  • htsjdk.variant.variantcontext.LazyGenotypesContext.LazyData
  • htsjdk.samtools.liftover.LiftOver
  • htsjdk.samtools.liftover.LiftOver.PartialLiftover
  • htsjdk.samtools.LinearIndex
  • htsjdk.tribble.index.linear.LinearIndex.ChrIndex (implements htsjdk.tribble.index.ChrIndex)
  • htsjdk.tribble.readers.LineReaderUtil
  • htsjdk.samtools.util.LocusComparator<T> (implements java.util.Comparator<T>)
  • htsjdk.samtools.util.LocusImpl (implements htsjdk.samtools.util.Locus)
  • htsjdk.samtools.util.Log
  • htsjdk.tribble.util.MathUtils
  • htsjdk.tribble.util.MathUtils.RunningStat
  • htsjdk.samtools.util.MergingIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
  • htsjdk.samtools.MergingSamRecordIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
  • htsjdk.samtools.metrics.MetricBase
    • htsjdk.samtools.SamFileValidator.ValidationMetrics
  • htsjdk.samtools.metrics.MetricsFile<BEAN,HKEY>
  • htsjdk.samtools.cram.common.MutableInt
  • htsjdk.samtools.filter.NotPrimaryAlignmentFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.NotPrimarySkippingIterator
  • htsjdk.samtools.cram.encoding.NullEncoding<T> (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.util.Objects
  • htsjdk.tribble.dbsnp.OldDbSNPFeature (implements htsjdk.tribble.Feature)
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • htsjdk.samtools.util.BlockCompressedOutputStream (implements htsjdk.samtools.util.LocationAware)
    • java.io.ByteArrayOutputStream
      • htsjdk.samtools.cram.io.ExposedByteArrayOutputStream
    • htsjdk.samtools.cram.io.DefaultBitOutputStream (implements htsjdk.samtools.cram.io.BitOutputStream)
    • java.io.FilterOutputStream
      • htsjdk.tribble.util.LittleEndianOutputStream
      • java.io.PrintStream (implements java.lang.Appendable, java.io.Closeable)
        • htsjdk.samtools.cram.common.NonforgivingPrintStream
    • htsjdk.samtools.util.Md5CalculatingOutputStream
    • htsjdk.samtools.cram.common.NullOutputStream
  • htsjdk.samtools.util.OverlapDetector<T>
  • htsjdk.samtools.cram.encoding.read_features.Padding (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.tribble.util.ParsingUtils
  • htsjdk.samtools.util.PeekableIterator<Object> (implements htsjdk.samtools.util.CloseableIterator<T>)
    • htsjdk.samtools.SamPairUtil.SetMateInfoIterator
  • htsjdk.samtools.util.PeekIterator<T> (implements java.util.Iterator<E>)
  • htsjdk.samtools.cram.lossy.PreservationPolicy
  • htsjdk.samtools.util.ProcessExecutor
  • htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
  • htsjdk.tribble.example.ProfileIndexReading
  • htsjdk.samtools.util.ProgressLogger (implements htsjdk.samtools.util.ProgressLoggerInterface)
  • htsjdk.samtools.util.QualityEncodingDetector
  • htsjdk.samtools.cram.lossy.QualityScorePreservation
  • htsjdk.samtools.cram.lossy.QualityScoreTreatment
  • htsjdk.samtools.util.QualityUtil
  • htsjdk.samtools.QueryInterval (implements java.lang.Comparable<T>)
  • htsjdk.samtools.cram.encoding.read_features.ReadBase (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.samtools.cram.lossy.ReadCategory
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • htsjdk.tribble.readers.LongLineBufferedReader
  • htsjdk.samtools.filter.ReadNameFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.cram.structure.ReadTag (implements java.lang.Comparable<T>)
  • htsjdk.samtools.reference.ReferenceSequence
  • htsjdk.samtools.reference.ReferenceSequenceFileFactory
  • htsjdk.samtools.reference.ReferenceSequenceFileWalker (implements java.io.Closeable)
  • htsjdk.samtools.cram.ref.ReferenceSource
  • htsjdk.samtools.cram.ref.ReferenceTracks
  • htsjdk.samtools.cram.mask.RefMaskUtils
  • htsjdk.samtools.cram.mask.RefMaskUtils.RefMask
  • htsjdk.samtools.cram.encoding.read_features.RefSkip (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.tribble.util.RemoteURLHelper (implements htsjdk.tribble.util.URLHelper)
  • htsjdk.samtools.ReservedTagConstants
  • htsjdk.samtools.util.ResourceLimitedMap<Key,Value>
    • htsjdk.samtools.util.FileAppendStreamLRUCache
  • htsjdk.samtools.cram.build.Sam2CramRecordFactory
  • htsjdk.samtools.SAMBinaryTagAndValue
    • htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue
  • htsjdk.samtools.SamFileHeaderMerger
  • htsjdk.samtools.SAMFileReader (implements htsjdk.samtools.SamReader, htsjdk.samtools.SamReader.Indexing)
    • htsjdk.samtools.SAMFileTruncatedReader
  • htsjdk.samtools.SAMFileReader.ReaderImplementation (implements htsjdk.samtools.SamReader.PrimitiveSamReader)
    • htsjdk.samtools.CRAMFileReader
  • htsjdk.samtools.SamFiles
  • htsjdk.samtools.SAMFileSource
  • htsjdk.samtools.SamFileValidator
  • htsjdk.samtools.SAMFileWriterFactory
  • htsjdk.samtools.SAMFileWriterImpl (implements htsjdk.samtools.SAMFileWriter)
    • htsjdk.samtools.CRAMFileWriter
    • htsjdk.samtools.SAMTextWriter
  • htsjdk.samtools.SAMHeaderRecordComparator<T> (implements java.util.Comparator<T>)
  • htsjdk.samtools.SamInputResource
  • htsjdk.samtools.SAMLineParser
  • htsjdk.samtools.util.SamLocusIterator (implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
  • htsjdk.samtools.util.SamLocusIterator.LocusInfo (implements htsjdk.samtools.util.Locus)
  • htsjdk.samtools.util.SamLocusIterator.RecordAndOffset
  • htsjdk.samtools.SamPairUtil
  • htsjdk.samtools.SamReader.AssertingIterator (implements htsjdk.samtools.SAMRecordIterator)
  • htsjdk.samtools.SamReader.PrimitiveSamReaderToSamReaderAdapter (implements htsjdk.samtools.SamReader, htsjdk.samtools.SamReader.Indexing)
  • htsjdk.samtools.SamReader.Type
  • htsjdk.samtools.SamReaderFactory
  • htsjdk.samtools.SAMRecord (implements java.lang.Cloneable)
    • htsjdk.samtools.BAMRecord
  • htsjdk.samtools.SAMRecord.SAMTagAndValue
  • htsjdk.samtools.SAMRecordCoordinateComparator (implements htsjdk.samtools.SAMRecordComparator)
  • htsjdk.samtools.util.SamRecordIntervalIteratorFactory
  • htsjdk.samtools.SAMRecordQueryNameComparator (implements htsjdk.samtools.SAMRecordComparator)
  • htsjdk.samtools.SAMRecordSetBuilder (implements java.lang.Iterable<T>)
  • htsjdk.samtools.util.SamRecordTrackingBuffer<T>
  • htsjdk.samtools.SAMRecordUtil
  • htsjdk.samtools.util.SamRecordWithOrdinal
  • htsjdk.samtools.SAMSequenceDictionary
  • htsjdk.variant.utils.SAMSequenceDictionaryExtractor
  • htsjdk.samtools.SAMSortOrderChecker
  • htsjdk.samtools.SamStreams
  • htsjdk.samtools.SAMTagUtil
  • htsjdk.samtools.SAMTestUtil
  • htsjdk.samtools.SAMTextHeaderCodec
  • htsjdk.samtools.SAMTools
  • htsjdk.samtools.SAMUtils
  • htsjdk.samtools.SAMValidationError
  • htsjdk.samtools.filter.SecondaryAlignmentFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.filter.SecondaryOrSupplementaryFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
  • htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
  • htsjdk.samtools.seekablestream.SeekableStreamFactory
  • htsjdk.samtools.util.SequenceUtil
  • htsjdk.tribble.bed.SimpleBEDFeature (implements htsjdk.tribble.bed.BEDFeature)
    • htsjdk.tribble.bed.FullBEDFeature (implements htsjdk.tribble.bed.BEDFeature)
  • htsjdk.samtools.cram.mask.SingleLineMaskReader (implements java.io.Closeable, htsjdk.samtools.cram.mask.ReadMaskReader)
  • htsjdk.samtools.cram.structure.Slice
  • htsjdk.samtools.cram.structure.SliceIO
  • htsjdk.samtools.util.SnappyLoader
  • htsjdk.samtools.cram.encoding.read_features.SoftClip (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.samtools.filter.SolexaNoiseFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.util.SolexaQualityConverter
  • htsjdk.samtools.util.SortingCollection<T> (implements java.lang.Iterable<T>)
  • htsjdk.samtools.util.SortingLongCollection
  • htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
  • htsjdk.samtools.SQTagUtil
  • htsjdk.samtools.util.StopWatch
  • htsjdk.samtools.metrics.StringHeader (implements htsjdk.samtools.metrics.Header)
  • htsjdk.samtools.util.StringLineReader (implements htsjdk.samtools.util.LineReader)
  • htsjdk.samtools.util.StringUtil
  • htsjdk.samtools.cram.encoding.SubexpIntegerEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.samtools.cram.encoding.read_features.Substitution (implements htsjdk.samtools.cram.encoding.read_features.ReadFeature, java.io.Serializable)
  • htsjdk.samtools.cram.structure.SubstitutionMatrix
  • htsjdk.tribble.index.tabix.TabixFormat (implements java.lang.Cloneable)
  • htsjdk.tribble.index.tabix.TabixIndex (implements htsjdk.tribble.index.Index)
  • htsjdk.tribble.index.tabix.TabixIndexCreator (implements htsjdk.tribble.index.IndexCreator)
  • htsjdk.tribble.readers.TabixIteratorLineReader (implements htsjdk.tribble.readers.LineReader)
  • htsjdk.tribble.readers.TabixReader
  • htsjdk.tribble.readers.TabixReader.TIndex
  • htsjdk.tribble.readers.TabixReader.TPair64 (implements java.lang.Comparable<T>)
  • htsjdk.tribble.util.TabixUtils
  • htsjdk.tribble.util.TabixUtils.TIndex
  • htsjdk.tribble.util.TabixUtils.TIntv
  • htsjdk.tribble.util.TabixUtils.TPair64 (implements java.lang.Comparable<T>)
  • htsjdk.samtools.filter.TagFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.TagValueAndUnsignedArrayFlag
  • htsjdk.samtools.cram.encoding.fastq.Template
  • htsjdk.samtools.cram.encoding.fastq.Template.ByteArrayHashWrapper
  • htsjdk.samtools.cram.encoding.fastq.Template.Segment
  • htsjdk.samtools.cram.encoding.fastq.Template.TemplateAssembler
  • htsjdk.samtools.cram.encoding.fastq.Template.TemplateHash
  • htsjdk.samtools.util.TempStreamFactory
  • htsjdk.samtools.util.TestUtil
  • htsjdk.samtools.TextCigarCodec
  • htsjdk.samtools.TextTagCodec
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • htsjdk.samtools.cram.mask.ReadMaskException
        • htsjdk.samtools.cram.mask.ReadMaskFormatException
      • java.lang.RuntimeException
        • htsjdk.tribble.exception.CodecLineParsingException
        • htsjdk.samtools.cram.common.NonforgivingPrintStream.PrintStreamError
        • htsjdk.samtools.SAMException
          • htsjdk.samtools.util.DateParser.InvalidDateException
          • htsjdk.samtools.FileTruncatedException
          • htsjdk.samtools.util.RuntimeEOFException
          • htsjdk.samtools.util.RuntimeIOException
          • htsjdk.samtools.SAMFormatException
          • htsjdk.samtools.util.SequenceUtil.SequenceListsDifferException
        • htsjdk.samtools.SAMTestUtil.SanityCheckFailedException
        • htsjdk.tribble.TribbleException
          • htsjdk.tribble.TribbleException.FeatureFileDoesntExist
          • htsjdk.tribble.TribbleException.InternalCodecException
          • htsjdk.tribble.TribbleException.InvalidDecodeLine
          • htsjdk.tribble.TribbleException.InvalidHeader
          • htsjdk.tribble.TribbleException.MalformedFeatureFile
          • htsjdk.tribble.TribbleException.TabixReaderFailure
          • htsjdk.tribble.TribbleException.UnableToCreateCorrectIndexType
          • htsjdk.tribble.TribbleException.UnableToReadIndexFile
        • htsjdk.tribble.exception.UnsortedFileException
  • htsjdk.samtools.apps.TimeChannel
  • htsjdk.samtools.apps.TimeRandomAccessFile
  • htsjdk.tribble.Tribble
  • htsjdk.tribble.index.TribbleIndexCreator (implements htsjdk.tribble.index.IndexCreator)
    • htsjdk.tribble.index.DynamicIndexCreator
    • htsjdk.tribble.index.interval.IntervalIndexCreator
    • htsjdk.tribble.index.linear.LinearIndexCreator
  • htsjdk.samtools.util.Tuple<A,B>
  • htsjdk.samtools.cram.encoding.UnaryIntegerEncoding (implements htsjdk.samtools.cram.encoding.Encoding<T>)
  • htsjdk.variant.variantcontext.VariantContext (implements htsjdk.tribble.Feature)
  • htsjdk.variant.variantcontext.VariantContextBuilder
  • htsjdk.variant.variantcontext.VariantContextComparator (implements java.util.Comparator<T>)
  • htsjdk.variant.variantcontext.VariantContextUtils
  • htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp
  • htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  • htsjdk.variant.variantcontext.writer.VariantContextWriterFactory
  • htsjdk.variant.vcf.VCFConstants
  • htsjdk.variant.vcf.VCFEncoder
  • htsjdk.variant.vcf.VCFFileReader (implements java.io.Closeable, java.lang.Iterable<T>)
  • htsjdk.variant.vcf.VCFHeader
  • htsjdk.variant.vcf.VCFHeaderLine (implements java.lang.Comparable<T>)
    • htsjdk.variant.vcf.VCFCompoundHeaderLine (implements htsjdk.variant.vcf.VCFIDHeaderLine)
      • htsjdk.variant.vcf.VCFFormatHeaderLine
      • htsjdk.variant.vcf.VCFInfoHeaderLine
    • htsjdk.variant.vcf.VCFSimpleHeaderLine (implements htsjdk.variant.vcf.VCFIDHeaderLine)
      • htsjdk.variant.vcf.VCFContigHeaderLine
      • htsjdk.variant.vcf.VCFFilterHeaderLine
  • htsjdk.variant.vcf.VCFHeaderLineTranslator
  • htsjdk.variant.vcf.VCFRecordCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
  • htsjdk.variant.vcf.VCFStandardHeaderLines
  • htsjdk.variant.vcf.VCFUtils
  • htsjdk.samtools.cram.common.Version (implements java.lang.Comparable<T>)
  • htsjdk.samtools.metrics.VersionHeader (implements htsjdk.samtools.metrics.Header)
  • htsjdk.samtools.util.WholeGenomeReferenceSequenceMask (implements htsjdk.samtools.util.ReferenceSequenceMask)
  • htsjdk.samtools.filter.WholeReadClippedFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  • htsjdk.samtools.cram.encoding.writer.Writer
  • java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
    • htsjdk.samtools.util.AsciiWriter

Interface Hierarchy

• htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders.Decoder
• htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
• htsjdk.samtools.cram.encoding.BitCodec<T>
• htsjdk.samtools.cram.io.BitInputStream
• htsjdk.samtools.cram.io.BitOutputStream
• htsjdk.tribble.index.ChrIndex
• java.lang.Cloneable
  • htsjdk.samtools.SAMFileSpan
  • htsjdk.samtools.util.SortingCollection.Codec<T>
• java.io.Closeable
  • htsjdk.samtools.BAMIndex
    • htsjdk.samtools.BrowseableBAMIndex
  • htsjdk.samtools.util.CloseableIterator<T> (also extends java.util.Iterator<E>)
    • htsjdk.tribble.CloseableTribbleIterator<T> (also extends java.lang.Iterable<T>)
    • htsjdk.samtools.SAMRecordIterator
  • htsjdk.samtools.fastq.FastqWriter
  • htsjdk.tribble.FeatureReader<T>
  • htsjdk.samtools.util.LineReader
  • htsjdk.tribble.readers.LineReader
  • htsjdk.samtools.reference.ReferenceSequenceFile
  • htsjdk.samtools.SAMFileWriter
  • htsjdk.samtools.SamReader (also extends java.lang.Iterable<T>)
  • htsjdk.variant.variantcontext.writer.VariantContextWriter
• htsjdk.samtools.util.CollectionUtil.DefaultingMap.Factory<V,K>
• java.util.Comparator<T>
  • htsjdk.samtools.SAMRecordComparator
• htsjdk.samtools.CoordinateSortedPairInfoMap.Codec<KEY,REC>
• htsjdk.samtools.CustomReaderFactory.ICustomReaderFactory
• htsjdk.samtools.cram.encoding.reader.DataReader<T>
• htsjdk.samtools.cram.encoding.writer.DataWriter<T>
• htsjdk.samtools.cram.encoding.Encoding<T>
• htsjdk.tribble.Feature
  • htsjdk.tribble.bed.BEDFeature
• htsjdk.tribble.FeatureCodec<FEATURE_TYPE,SOURCE>
• htsjdk.samtools.metrics.Header
• htsjdk.tribble.index.Index
  • htsjdk.tribble.index.MutableIndex
• htsjdk.tribble.index.IndexCreator
• htsjdk.samtools.seekablestream.ISeekableStreamFactory
• java.lang.Iterable<T>
  • htsjdk.tribble.CloseableTribbleIterator<T> (also extends htsjdk.samtools.util.CloseableIterator<T>)
  • htsjdk.samtools.SamReader (also extends java.io.Closeable)
• java.util.Iterator<E>
  • htsjdk.samtools.util.CloseableIterator<T> (also extends java.io.Closeable)
    • htsjdk.tribble.CloseableTribbleIterator<T> (also extends java.lang.Iterable<T>)
    • htsjdk.samtools.SAMRecordIterator
  • htsjdk.tribble.readers.LineIterator
• htsjdk.samtools.util.Lazy.LazyInitializer<T>
• htsjdk.variant.variantcontext.LazyGenotypesContext.LazyParser
• htsjdk.samtools.util.LocationAware
  • htsjdk.tribble.readers.Positional
• htsjdk.samtools.util.Locus
• htsjdk.tribble.NameAwareCodec
• htsjdk.samtools.cram.mask.PositionMask
• htsjdk.samtools.util.ProgressLoggerInterface
• htsjdk.samtools.cram.encoding.read_features.ReadFeature
• htsjdk.samtools.cram.mask.ReadMaskFactory<T>
• htsjdk.samtools.cram.mask.ReadMaskReader
• htsjdk.samtools.util.ReferenceSequenceMask
• htsjdk.samtools.util.ResourceLimitedMapFunctor<Key,Value>
• htsjdk.samtools.SamReader.Indexing
• htsjdk.samtools.SamReader.PrimitiveSamReader
• htsjdk.samtools.SAMRecordFactory
• htsjdk.samtools.filter.SamRecordFilter
• htsjdk.tribble.readers.TabixReader.Iterator
• htsjdk.tribble.util.URLHelper
• htsjdk.samtools.seekablestream.UserPasswordInput
• htsjdk.variant.vcf.VCFIDHeaderLine

Annotation Type Hierarchy

• htsjdk.samtools.cram.encoding.DataSeries (implements java.lang.annotation.Annotation)
• htsjdk.samtools.cram.encoding.DataSeriesMap (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • htsjdk.samtools.CigarOperator
    • htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy
    • htsjdk.samtools.SAMFileHeader.SortOrder
    • htsjdk.samtools.SAMFileHeader.GroupOrder
    • htsjdk.samtools.SAMTag
    • htsjdk.samtools.SAMValidationError.Severity
    • htsjdk.samtools.SAMValidationError.Type
    • htsjdk.samtools.SQTagUtil.SQBase
    • htsjdk.samtools.SamPairUtil.PairOrientation
    • htsjdk.samtools.SamReaderFactory.Option
    • htsjdk.samtools.ValidationStringency
    • htsjdk.samtools.cram.encoding.DataSeriesType
    • htsjdk.samtools.cram.lossy.BaseCategoryType
    • htsjdk.samtools.cram.lossy.QualityScoreTreatmentType
    • htsjdk.samtools.cram.lossy.ReadCategoryType
    • htsjdk.samtools.cram.structure.BlockCompressionMethod
    • htsjdk.samtools.cram.structure.BlockContentType
    • htsjdk.samtools.cram.structure.EncodingID
    • htsjdk.samtools.cram.structure.EncodingKey
    • htsjdk.samtools.util.BlockCompressedInputStream.FileTermination
    • htsjdk.samtools.util.FastqQualityFormat
    • htsjdk.samtools.util.Log.LogLevel
    • htsjdk.samtools.util.QualityEncodingDetector.FileContext
    • htsjdk.tribble.annotation.Strand
    • htsjdk.tribble.bed.BEDCodec.StartOffset
    • htsjdk.tribble.gelitext.DiploidGenotype
    • htsjdk.tribble.index.AbstractIndex.IndexType
    • htsjdk.tribble.index.IndexFactory.IndexBalanceApproach
    • htsjdk.tribble.index.IndexFactory.IndexType
    • htsjdk.tribble.readers.LineReaderUtil.LineReaderOption
    • htsjdk.variant.bcf2.BCF2Type
    • htsjdk.variant.variantcontext.GenotypeType
    • htsjdk.variant.variantcontext.VariantContext.Validation
    • htsjdk.variant.variantcontext.VariantContext.Type
    • htsjdk.variant.variantcontext.writer.Options
    • htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType
    • htsjdk.variant.vcf.VCFCompoundHeaderLine.SupportedHeaderLineType
    • htsjdk.variant.vcf.VCFHeader.HEADER_FIELDS
    • htsjdk.variant.vcf.VCFHeaderLineCount
    • htsjdk.variant.vcf.VCFHeaderLineType
    • htsjdk.variant.vcf.VCFHeaderVersion