# Hierarchy For All Packages

Package Hierarchies:

- htsjdk.annotations,
- htsjdk.beta.codecs.hapref.fasta,
- htsjdk.beta.codecs.reads,
- htsjdk.beta.codecs.reads.bam,
- htsjdk.beta.codecs.reads.bam.bamV1_0,
- htsjdk.beta.codecs.reads.cram,
- htsjdk.beta.codecs.reads.cram.cramV2_1,
- htsjdk.beta.codecs.reads.cram.cramV3_0,
- htsjdk.beta.codecs.reads.cram.cramV3_1,
- htsjdk.beta.codecs.reads.htsget,
- htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2,
- htsjdk.beta.codecs.reads.sam,
- htsjdk.beta.codecs.reads.sam.samV1_0,
- htsjdk.beta.codecs.variants.vcf,
- htsjdk.beta.codecs.variants.vcf.vcfv3_2,
- htsjdk.beta.codecs.variants.vcf.vcfv3_3,
- htsjdk.beta.codecs.variants.vcf.vcfv4_0,
- htsjdk.beta.codecs.variants.vcf.vcfv4_1,
- htsjdk.beta.codecs.variants.vcf.vcfv4_2,
- htsjdk.beta.codecs.variants.vcf.vcfv4_3,
- htsjdk.beta.exception,
- htsjdk.beta.io,
- htsjdk.beta.io.bundle,
- htsjdk.beta.plugin,
- htsjdk.beta.plugin.hapref,
- htsjdk.beta.plugin.interval,
- htsjdk.beta.plugin.reads,
- htsjdk.beta.plugin.registry,
- htsjdk.beta.plugin.variants,
- htsjdk.io,
- htsjdk.samtools,
- htsjdk.samtools.apps,
- htsjdk.samtools.cram,
- htsjdk.samtools.cram.build,
- htsjdk.samtools.cram.common,
- htsjdk.samtools.cram.compression,
- htsjdk.samtools.cram.compression.fqzcomp,
- htsjdk.samtools.cram.compression.nametokenisation,
- htsjdk.samtools.cram.compression.nametokenisation.tokens,
- htsjdk.samtools.cram.compression.range,
- htsjdk.samtools.cram.compression.rans,
- htsjdk.samtools.cram.digest,
- htsjdk.samtools.cram.encoding,
- htsjdk.samtools.cram.encoding.core,
- htsjdk.samtools.cram.encoding.core.experimental,
- htsjdk.samtools.cram.encoding.core.huffmanUtils,
- htsjdk.samtools.cram.encoding.external,
- htsjdk.samtools.cram.encoding.reader,
- htsjdk.samtools.cram.encoding.readfeatures,
- htsjdk.samtools.cram.encoding.writer,
- htsjdk.samtools.cram.io,
- htsjdk.samtools.cram.ref,
- htsjdk.samtools.cram.structure,
- htsjdk.samtools.cram.structure.block,
- 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.htsget,
- htsjdk.samtools.util.nio,
- htsjdk.samtools.util.zip,
- htsjdk.tribble,
- htsjdk.tribble.annotation,
- htsjdk.tribble.bed,
- htsjdk.tribble.example,
- htsjdk.tribble.exception,
- htsjdk.tribble.gff,
- htsjdk.tribble.index,
- htsjdk.tribble.index.interval,
- htsjdk.tribble.index.linear,
- htsjdk.tribble.index.tabix,
- htsjdk.tribble.IntervalList,
- htsjdk.tribble.readers,
- htsjdk.tribble.util,
- htsjdk.tribble.util.popgen,
- htsjdk.utils,
- htsjdk.variant.bcf2,
- htsjdk.variant.example,
- htsjdk.variant.utils,
- htsjdk.variant.variantcontext,
- htsjdk.variant.variantcontext.filter,
- 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.CSIIndex (implements htsjdk.samtools.BrowseableBAMIndex)
    - htsjdk.samtools.DiskBasedBAMFileIndex
  - java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    - java.util.AbstractList<E> (implements java.util.List<E>)
      - java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        - htsjdk.variant.variantcontext.filter.CompoundFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
  - 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.IntervalList.IntervalListCodec
    - htsjdk.tribble.gff.Gff3Codec
  - 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)
  - htsjdk.samtools.filter.AbstractJavascriptFilter<HEADER,TYPE>
    - htsjdk.samtools.filter.JavascriptSamRecordFilter (implements htsjdk.samtools.filter.SamRecordFilter)
    - htsjdk.variant.variantcontext.filter.JavascriptVariantFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
  - htsjdk.samtools.util.AbstractLocusInfo<E> (implements htsjdk.samtools.util.Locatable, htsjdk.samtools.util.Locus)
    - htsjdk.samtools.util.SamLocusIterator.LocusInfo
  - htsjdk.samtools.util.AbstractLocusIterator<T,K> (implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
    - htsjdk.samtools.util.EdgeReadIterator
    - htsjdk.samtools.util.SamLocusIterator
  - 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>
  - htsjdk.samtools.util.AbstractProgressLogger (implements htsjdk.samtools.util.ProgressLoggerInterface)
    - htsjdk.samtools.util.ProgressLogger
  - htsjdk.samtools.util.AbstractRecordAndOffset
    - htsjdk.samtools.util.EdgingRecordAndOffset
    - htsjdk.samtools.util.SamLocusIterator.RecordAndOffset
  - htsjdk.samtools.AbstractSAMHeaderRecord (implements java.io.Serializable)
    - htsjdk.samtools.SAMFileHeader (implements htsjdk.beta.plugin.HtsHeader)
    - htsjdk.samtools.SAMProgramRecord
    - htsjdk.samtools.SAMReadGroupRecord
    - htsjdk.samtools.SAMSequenceRecord (implements java.lang.Cloneable, htsjdk.samtools.util.Locatable)
  - htsjdk.samtools.filter.AggregateFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.samtools.filter.AlignedFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.samtools.AlignmentBlock (implements java.io.Serializable)
  - htsjdk.samtools.cram.structure.AlignmentContext
  - htsjdk.samtools.cram.structure.AlignmentSpan
  - htsjdk.tribble.index.tabix.AllRefsTabixIndexCreator (implements htsjdk.tribble.index.IndexCreator)
    - htsjdk.tribble.index.tabix.StreamBasedTabixIndexCreator
  - 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.samtools.util.AsyncBufferedIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
  - htsjdk.io.AsyncWriterPool (implements java.io.Closeable)
  - htsjdk.samtools.cram.BAIEntry (implements java.lang.Comparable<T>)
  - htsjdk.beta.codecs.reads.bam.BAMCodec (implements htsjdk.beta.plugin.reads.ReadsCodec)
    - htsjdk.beta.codecs.reads.bam.bamV1_0.BAMCodecV1_0
  - htsjdk.samtools.BamConverter
  - htsjdk.beta.codecs.reads.bam.BAMDecoder (implements htsjdk.beta.plugin.reads.ReadsDecoder)
    - htsjdk.beta.codecs.reads.bam.bamV1_0.BAMDecoderV1_0
  - htsjdk.beta.codecs.reads.bam.BAMDecoderOptions
  - htsjdk.beta.codecs.reads.bam.BAMEncoder (implements htsjdk.beta.plugin.reads.ReadsEncoder)
    - htsjdk.beta.codecs.reads.bam.bamV1_0.BAMEncoderV1_0
  - htsjdk.beta.codecs.reads.bam.BAMEncoderOptions
  - htsjdk.samtools.BamFileIoUtils
  - htsjdk.samtools.BAMFileReader.BAMQueryFilteringIterator
  - htsjdk.samtools.BAMFileSpan (implements htsjdk.samtools.SAMFileSpan, java.io.Serializable)
  - htsjdk.samtools.BAMIndexer
  - htsjdk.samtools.BAMIndexMetaData
  - htsjdk.samtools.BamIndexValidator
  - htsjdk.samtools.BAMQueryMultipleIntervalsIteratorFilter
  - htsjdk.samtools.BAMRecordCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
  - htsjdk.samtools.BAMSBIIndexer
  - htsjdk.samtools.BAMStartingAtIteratorFilter
  - htsjdk.samtools.BAMStreamWriter
  - htsjdk.samtools.cram.encoding.readfeatures.BaseQualityScore (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - htsjdk.samtools.cram.encoding.readfeatures.Bases (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - htsjdk.samtools.fastq.BasicFastqWriter (implements htsjdk.samtools.fastq.FastqWriter, java.io.Flushable)
  - 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.Bin (implements java.lang.Comparable<T>)
    - htsjdk.samtools.BinWithOffset
  - 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.BinaryTagCodec
  - htsjdk.samtools.BinList (implements java.lang.Iterable<T>)
  - htsjdk.samtools.BinningIndexBuilder
  - htsjdk.samtools.BinningIndexContent
  - htsjdk.samtools.BinningIndexContent.BinList (implements java.lang.Iterable<T>)
  - htsjdk.variant.utils.BinomialCoefficientUtil
  - htsjdk.samtools.cram.structure.block.Block
  - htsjdk.tribble.index.Block
  - htsjdk.samtools.util.BlockCompressedFilePointerUtil
  - htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile
  - htsjdk.samtools.util.BlockCompressedInputStream.DecompressedBlock
  - htsjdk.samtools.util.BlockCompressedStreamConstants
  - htsjdk.samtools.util.BlockGunzipper
  - htsjdk.beta.io.bundle.Bundle (implements java.lang.Iterable<T>, java.io.Serializable)
    - htsjdk.beta.plugin.reads.ReadsBundle<T> (implements java.io.Serializable)
    - htsjdk.beta.plugin.variants.VariantsBundle (implements java.io.Serializable)
  - htsjdk.beta.io.bundle.BundleBuilder
  - htsjdk.beta.io.bundle.BundleJSON
  - htsjdk.beta.io.bundle.BundleResourceBase (implements htsjdk.beta.io.bundle.BundleResource, java.io.Serializable)
    - htsjdk.beta.io.bundle.InputStreamResource
      - htsjdk.beta.io.bundle.SeekableStreamResource
    - htsjdk.beta.io.bundle.IOPathResource (implements java.io.Serializable)
    - htsjdk.beta.io.bundle.OutputStreamResource
  - htsjdk.beta.io.bundle.BundleResourceType
  - htsjdk.samtools.cram.compression.range.ByteModel
  - htsjdk.samtools.Chunk (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
  - htsjdk.samtools.Cigar (implements java.lang.Iterable<T>, java.io.Serializable)
  - htsjdk.samtools.CigarElement (implements java.io.Serializable)
  - htsjdk.samtools.util.CigarUtil
  - htsjdk.utils.ClassFinder
  - htsjdk.samtools.util.CloserUtil
  - htsjdk.samtools.util.CodeUtil
  - htsjdk.samtools.util.CollectionUtil
  - htsjdk.samtools.util.CollectionUtil.Partitioner<V,K>
  - htsjdk.variant.variantcontext.CommonInfo (implements java.io.Serializable)
  - htsjdk.samtools.cram.structure.CompressionHeader
  - htsjdk.samtools.cram.structure.CompressionHeaderEncodingMap
  - htsjdk.samtools.cram.build.CompressionHeaderFactory
  - htsjdk.samtools.cram.compression.CompressionUtils
  - htsjdk.samtools.cram.structure.CompressorCache
  - htsjdk.samtools.cram.compression.range.Constants
  - htsjdk.samtools.cram.compression.rans.Constants
  - htsjdk.samtools.cram.structure.Container
  - htsjdk.samtools.cram.build.ContainerFactory
  - htsjdk.samtools.cram.structure.ContainerHeader
  - htsjdk.samtools.cram.digest.ContentDigests
  - htsjdk.samtools.CoordinateSortedPairInfoMap<KEY,REC> (implements java.lang.Iterable<T>)
  - htsjdk.samtools.util.CoordMath
  - htsjdk.samtools.cram.encoding.core.CoreCodec<T> (implements htsjdk.samtools.cram.encoding.CRAMCodec<T>)
    - htsjdk.samtools.cram.encoding.core.BetaIntegerCodec
  - htsjdk.tribble.example.CountRecords
  - htsjdk.samtools.cram.CRAIEntry (implements java.lang.Comparable<T>)
  - htsjdk.samtools.cram.CRAIIndex
  - htsjdk.samtools.CRAMBAIIndexer (implements htsjdk.samtools.CRAMIndexer)
  - htsjdk.samtools.cram.io.CRAMByteReader
  - htsjdk.samtools.cram.io.CRAMByteWriter
  - htsjdk.beta.codecs.reads.cram.CRAMCodec (implements htsjdk.beta.plugin.reads.ReadsCodec)
    - htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMCodecV2_1
    - htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMCodecV3_0
    - htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMCodecV3_1
  - htsjdk.samtools.cram.structure.CRAMCodecModelContext
  - htsjdk.samtools.cram.CramComparison
  - htsjdk.samtools.cram.structure.CRAMCompressionRecord
  - htsjdk.samtools.cram.build.CramContainerIterator (implements java.io.Closeable, java.util.Iterator<E>)
    - htsjdk.samtools.cram.build.CramContainerHeaderIterator
    - htsjdk.samtools.cram.build.CramSpanContainerIterator
  - htsjdk.samtools.CRAMContainerStreamWriter
  - htsjdk.samtools.cram.CramConverter
  - htsjdk.samtools.CRAMCRAIIndexer (implements htsjdk.samtools.CRAMIndexer)
  - htsjdk.beta.codecs.reads.cram.CRAMDecoder (implements htsjdk.beta.plugin.reads.ReadsDecoder)
    - htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMDecoderV2_1
    - htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMDecoderV3_0
    - htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMDecoderV3_1
  - htsjdk.beta.codecs.reads.cram.CRAMDecoderOptions
  - htsjdk.beta.codecs.reads.cram.CRAMEncoder (implements htsjdk.beta.plugin.reads.ReadsEncoder)
    - htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMEncoderV2_1
    - htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMEncoderV3_0
    - htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMEncoderV3_1
  - htsjdk.beta.codecs.reads.cram.CRAMEncoderOptions
  - htsjdk.samtools.cram.encoding.CRAMEncoding<T>
    - htsjdk.samtools.cram.encoding.core.BetaIntegerEncoding
    - htsjdk.samtools.cram.encoding.ByteArrayLenEncoding
    - htsjdk.samtools.cram.encoding.external.ByteArrayStopEncoding
    - htsjdk.samtools.cram.encoding.core.CanonicalHuffmanByteEncoding
    - htsjdk.samtools.cram.encoding.core.CanonicalHuffmanIntegerEncoding
    - htsjdk.samtools.cram.encoding.external.ExternalEncoding<T>
      - htsjdk.samtools.cram.encoding.external.ExternalByteArrayEncoding
      - htsjdk.samtools.cram.encoding.external.ExternalByteEncoding
      - htsjdk.samtools.cram.encoding.external.ExternalIntegerEncoding
      - htsjdk.samtools.cram.encoding.external.ExternalLongEncoding
    - htsjdk.samtools.cram.encoding.core.GammaIntegerEncoding
    - htsjdk.samtools.cram.encoding.core.experimental.GolombIntegerEncoding
    - htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding
    - htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding
    - htsjdk.samtools.cram.encoding.core.SubexponentialIntegerEncoding
  - htsjdk.samtools.cram.structure.CRAMEncodingStrategy
  - htsjdk.samtools.cram.structure.CramHeader
  - htsjdk.samtools.cram.io.CramInt
  - htsjdk.samtools.cram.io.CramIntArray
  - htsjdk.samtools.cram.build.CramIO
  - htsjdk.samtools.CRAMIterator (implements java.io.Closeable, htsjdk.samtools.SAMRecordIterator)
  - htsjdk.samtools.cram.ref.CRAMLazyReferenceSource (implements htsjdk.samtools.cram.ref.CRAMReferenceSource)
  - htsjdk.samtools.cram.encoding.reader.CramRecordReader
  - htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
  - htsjdk.samtools.cram.structure.CRAMRecordReadFeatures.DecodeResult
  - htsjdk.samtools.cram.encoding.writer.CramRecordWriter
  - htsjdk.samtools.cram.build.CRAMReferenceRegion
  - htsjdk.samtools.cram.CramStats
  - htsjdk.samtools.cram.common.CRAMVersion (implements java.lang.Comparable<T>)
  - htsjdk.samtools.cram.common.CramVersions
  - htsjdk.samtools.CustomReaderFactory
  - htsjdk.samtools.cram.encoding.reader.DataSeriesReader<T>
  - htsjdk.samtools.cram.encoding.writer.DataSeriesWriter<T>
  - 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.Defaults
  - htsjdk.samtools.DefaultSAMRecordFactory (implements htsjdk.samtools.SAMRecordFactory)
  - htsjdk.samtools.util.zip.DeflaterFactory
  - htsjdk.samtools.util.DelegatingIterator<T> (implements htsjdk.samtools.util.CloseableIterator<T>)
  - htsjdk.samtools.util.nio.DeleteOnExitPathHook
  - htsjdk.samtools.cram.encoding.readfeatures.Deletion (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - htsjdk.samtools.util.DiskBackedQueue<E> (implements java.util.Queue<E>)
  - htsjdk.samtools.DownsamplingIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
  - htsjdk.samtools.DownsamplingIteratorFactory
  - htsjdk.samtools.filter.DuplicateReadFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.samtools.DuplicateScoringStrategy
  - htsjdk.samtools.DuplicateSet
  - htsjdk.samtools.DuplicateSetIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
  - htsjdk.samtools.cram.ref.EnaRefService
  - htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken
    - htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken.DupOrDiffToken
    - htsjdk.samtools.cram.compression.nametokenisation.tokens.EncodeToken.EndToken
  - htsjdk.samtools.cram.structure.EncodingDescriptor
  - htsjdk.samtools.cram.encoding.EncodingFactory
  - htsjdk.samtools.example.ExampleSamUsage
  - htsjdk.samtools.cram.encoding.external.ExternalByteArrayCodec
  - htsjdk.samtools.cram.compression.ExternalCompressor
    - htsjdk.samtools.cram.compression.BZIP2ExternalCompressor
    - htsjdk.samtools.cram.compression.fqzcomp.FQZCompExternalCompressor
    - htsjdk.samtools.cram.compression.GZIPExternalCompressor
    - htsjdk.samtools.cram.compression.LZMAExternalCompressor
    - htsjdk.samtools.cram.compression.nametokenisation.NameTokeniserExternalCompressor
    - htsjdk.samtools.cram.compression.range.RangeExternalCompressor
    - htsjdk.samtools.cram.compression.RANS4x8ExternalCompressor
    - htsjdk.samtools.cram.compression.RANSNx16ExternalCompressor
    - htsjdk.samtools.cram.compression.RAWExternalCompressor
    - htsjdk.samtools.cram.compression.TrialCompressor
  - htsjdk.samtools.filter.FailsVendorReadQualityFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0 (implements htsjdk.beta.plugin.hapref.HaploidReferenceCodec)
  - htsjdk.beta.codecs.hapref.fasta.FASTADecoderV1_0 (implements htsjdk.beta.plugin.hapref.HaploidReferenceDecoder)
  - htsjdk.samtools.reference.FastaReferenceWriter (implements java.lang.AutoCloseable)
  - htsjdk.samtools.reference.FastaReferenceWriterBuilder
  - htsjdk.samtools.reference.FastaSequenceFile
  - htsjdk.samtools.reference.FastaSequenceIndex (implements java.lang.Iterable<T>)
  - htsjdk.samtools.reference.FastaSequenceIndexCreator
  - htsjdk.samtools.reference.FastaSequenceIndexEntry
  - htsjdk.samtools.util.FastLineReader (implements java.io.Closeable)
  - htsjdk.samtools.fastq.FastqConstants
  - htsjdk.samtools.fastq.FastqEncoder
  - htsjdk.samtools.fastq.FastqReader (implements java.io.Closeable, java.lang.Iterable<T>, java.util.Iterator<E>)
  - htsjdk.samtools.fastq.FastqRecord (implements java.io.Serializable)
  - htsjdk.samtools.fastq.FastqWriterFactory
  - htsjdk.tribble.FeatureCodecHeader
  - htsjdk.samtools.util.FileExtensions
  - htsjdk.samtools.filter.FilteringSamIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
    - htsjdk.samtools.filter.FilteringIterator
  - htsjdk.variant.variantcontext.filter.FilteringVariantContextIterator (implements htsjdk.samtools.util.CloseableIterator<T>, java.lang.Iterable<T>)
    - htsjdk.variant.variantcontext.filter.FilteringIterator
  - htsjdk.samtools.util.FormatUtil
  - htsjdk.samtools.cram.compression.fqzcomp.FQZCompDecode
  - htsjdk.samtools.cram.compression.fqzcomp.FQZCompEncode
  - htsjdk.samtools.cram.compression.fqzcomp.FQZGlobalFlags
  - htsjdk.samtools.cram.compression.fqzcomp.FQZModels
  - htsjdk.samtools.cram.compression.fqzcomp.FQZParam
  - htsjdk.samtools.cram.compression.fqzcomp.FQZParams
  - htsjdk.samtools.cram.compression.fqzcomp.FQZState
  - htsjdk.samtools.cram.compression.fqzcomp.FQZUtils
  - 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.variant.utils.GeneralUtils
  - htsjdk.samtools.GenomicIndexUtil
  - htsjdk.variant.variantcontext.Genotype (implements java.lang.Comparable<T>, java.io.Serializable)
    - htsjdk.variant.variantcontext.FastGenotype
  - htsjdk.variant.variantcontext.GenotypeBuilder
  - htsjdk.variant.variantcontext.GenotypeJEXLContext
  - htsjdk.variant.variantcontext.GenotypeLikelihoods
  - htsjdk.variant.variantcontext.GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
  - htsjdk.variant.variantcontext.filter.GenotypeQualityFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
  - htsjdk.variant.variantcontext.GenotypesContext (implements java.util.List<E>, java.io.Serializable)
    - htsjdk.variant.variantcontext.LazyGenotypesContext
  - htsjdk.tribble.gff.Gff3BaseData (implements htsjdk.samtools.util.Locatable)
  - htsjdk.tribble.gff.Gff3Constants
  - htsjdk.tribble.gff.Gff3FeatureImpl (implements htsjdk.tribble.gff.Gff3Feature)
  - htsjdk.tribble.gff.Gff3Writer (implements java.io.Closeable)
  - htsjdk.samtools.util.GZIIndex
  - htsjdk.samtools.util.GZIIndex.GZIIndexer (implements java.io.Closeable)
  - htsjdk.samtools.util.GZIIndex.IndexEntry
  - htsjdk.samtools.util.GzipCodec
  - htsjdk.beta.plugin.hapref.HaploidReferenceDecoderOptions (implements htsjdk.beta.plugin.HtsDecoderOptions)
  - htsjdk.beta.plugin.hapref.HaploidReferenceEncoderOptions (implements htsjdk.beta.plugin.HtsEncoderOptions)
  - htsjdk.beta.plugin.hapref.HaploidReferenceFormats
  - htsjdk.beta.plugin.hapref.HapRefDecoderOptions (implements htsjdk.beta.plugin.HtsDecoderOptions)
  - htsjdk.samtools.cram.encoding.readfeatures.HardClip (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - htsjdk.tribble.util.popgen.HardyWeinbergCalculation
  - htsjdk.variant.variantcontext.filter.HeterozygosityFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
  - htsjdk.samtools.util.Histogram<K> (implements java.io.Serializable)
  - htsjdk.samtools.util.Histogram.Bin<K> (implements java.io.Serializable)
  - htsjdk.beta.plugin.registry.HtsCodecRegistry
  - htsjdk.beta.plugin.registry.HtsCodecResolver<C>
    - htsjdk.beta.plugin.registry.HaploidReferenceResolver
    - htsjdk.beta.plugin.registry.ReadsResolver
    - htsjdk.beta.plugin.registry.VariantsResolver
  - htsjdk.beta.plugin.registry.HtsDefaultRegistry
  - htsjdk.beta.codecs.reads.htsget.HtsgetBAMCodec (implements htsjdk.beta.plugin.reads.ReadsCodec)
    - htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMCodecV1_2
  - htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder (implements htsjdk.beta.plugin.reads.ReadsDecoder)
    - htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
  - htsjdk.samtools.HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.samtools.util.htsget.HtsgetErrorResponse
  - htsjdk.samtools.util.htsget.HtsgetRequest
    - htsjdk.samtools.util.htsget.HtsgetPOSTRequest
  - htsjdk.samtools.util.htsget.HtsgetResponse
  - htsjdk.samtools.util.htsget.HtsgetResponse.Block
  - htsjdk.beta.plugin.interval.HtsIntervalUtils
  - htsjdk.io.HtsPath (implements htsjdk.io.IOPath, java.io.Serializable)
  - htsjdk.beta.plugin.interval.HtsQueryInterval (implements htsjdk.beta.plugin.interval.HtsInterval)
  - htsjdk.beta.plugin.HtsVersion (implements java.lang.Comparable<T>)
  - htsjdk.tribble.util.HTTPHelper (implements htsjdk.tribble.util.URLHelper)
  - htsjdk.samtools.util.HttpUtils
  - htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanBitCode<T>
  - htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanCanoncialCodeGenerator<T>
  - htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParams<T>
  - htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanParamsCalculator<T>
  - htsjdk.samtools.reference.IndexedFastaSequenceFile
  - htsjdk.tribble.index.IndexFactory
  - htsjdk.samtools.IndexMerger<T>
    - htsjdk.samtools.BAMIndexMerger
    - htsjdk.samtools.cram.CRAIIndexMerger
    - htsjdk.samtools.SBIIndexMerger
    - htsjdk.tribble.index.tabix.TabixIndexMerger
  - htsjdk.tribble.example.IndexToTable
  - htsjdk.tribble.example.IndicesAreEqual
  - htsjdk.samtools.util.zip.InflaterFactory
  - java.io.InputStream (implements java.io.Closeable)
    - htsjdk.samtools.util.BlockCompressedInputStream (implements htsjdk.samtools.util.LocationAware)
      - htsjdk.samtools.util.AsyncBlockCompressedInputStream
    - java.io.ByteArrayInputStream
      - htsjdk.beta.io.bundle.SignatureStream
    - htsjdk.samtools.util.CoordSpanInputSteam
    - htsjdk.samtools.cram.io.CountingInputStream
    - htsjdk.samtools.cram.io.CRC32InputStream
    - 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.ByteArraySeekableStream
      - htsjdk.samtools.seekablestream.SeekableBufferedStream
      - htsjdk.samtools.seekablestream.SeekableFileStream
      - htsjdk.samtools.seekablestream.SeekableFTPStream
      - htsjdk.samtools.seekablestream.SeekableHTTPStream
      - htsjdk.samtools.seekablestream.SeekableMemoryStream
      - htsjdk.samtools.seekablestream.SeekablePathStream
  - htsjdk.samtools.cram.io.InputStreamUtils
  - htsjdk.samtools.cram.encoding.readfeatures.InsertBase (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - htsjdk.samtools.cram.encoding.readfeatures.Insertion (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - htsjdk.samtools.filter.InsertSizeFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.samtools.util.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>, htsjdk.tribble.NamedFeature)
  - htsjdk.tribble.index.interval.Interval (implements java.lang.Comparable<T>)
  - htsjdk.samtools.util.IntervalCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
  - htsjdk.samtools.util.IntervalCoordinateComparator (implements java.util.Comparator<T>, java.io.Serializable)
  - htsjdk.samtools.filter.IntervalFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.samtools.filter.IntervalKeepPairFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.samtools.util.IntervalList (implements java.lang.Iterable<T>)
  - htsjdk.samtools.util.IntervalList.IntervalMergerIterator (implements java.util.Iterator<E>)
  - htsjdk.samtools.util.IntervalListReferenceSequenceMask (implements htsjdk.samtools.util.ReferenceSequenceMask)
  - htsjdk.samtools.util.IntervalListWriter (implements java.io.Closeable)
  - 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.samtools.util.IntervalUtil.IntervalCombiner
  - 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.filter.InvertFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.beta.io.IOPathUtils
  - htsjdk.samtools.util.IOUtil
  - htsjdk.beta.plugin.IOUtils
  - 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.reference.SamLocusAndReferenceIterator
  - htsjdk.samtools.util.Iterables
  - htsjdk.samtools.cram.io.ITF8
  - 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.samtools.util.LocusComparator<T> (implements java.util.Comparator<T>, java.io.Serializable)
  - htsjdk.samtools.util.LocusImpl (implements htsjdk.samtools.util.Locus)
  - htsjdk.samtools.util.Log
  - htsjdk.samtools.cram.io.LTF8
  - htsjdk.samtools.filter.MappingQualityFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - 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> (implements java.io.Serializable)
  - htsjdk.samtools.util.Murmur3 (implements java.io.Serializable)
  - htsjdk.tribble.MutableFeature (implements htsjdk.tribble.Feature)
  - htsjdk.samtools.cram.common.MutableInt
  - htsjdk.samtools.cram.compression.nametokenisation.NameTokenisationDecode
  - htsjdk.samtools.cram.compression.nametokenisation.NameTokenisationEncode
  - java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    - htsjdk.samtools.util.BlockCompressedOutputStream (implements htsjdk.samtools.util.LocationAware)
      - htsjdk.samtools.util.TerminatorlessBlockCompressedOutputStream
    - htsjdk.samtools.cram.io.DefaultBitOutputStream (implements htsjdk.samtools.cram.io.BitOutputStream)
    - java.io.FilterOutputStream
      - htsjdk.samtools.cram.io.CRC32OutputStream
      - java.util.zip.DeflaterOutputStream
        - java.util.zip.GZIPOutputStream
          - htsjdk.samtools.util.CustomGzipOutputStream
      - htsjdk.tribble.util.LittleEndianOutputStream
    - htsjdk.samtools.util.Md5CalculatingOutputStream
    - htsjdk.samtools.util.PositionalOutputStream (implements htsjdk.samtools.util.LocationAware)
  - htsjdk.samtools.filter.OverclippedReadFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.samtools.util.OverlapDetector<T>
  - htsjdk.samtools.cram.encoding.readfeatures.Padding (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - htsjdk.tribble.util.ParsingUtils
  - htsjdk.variant.variantcontext.filter.PassingVariantFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
  - 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.example.PrintReadsExample
  - htsjdk.variant.example.PrintVariantsExample
  - htsjdk.samtools.util.ProcessExecutor
  - htsjdk.samtools.util.ProcessExecutor.ExitStatusAndOutput
  - htsjdk.tribble.example.ProfileIndexReading
  - htsjdk.samtools.util.QualityEncodingDetector
  - htsjdk.samtools.util.QualityUtil
  - htsjdk.samtools.QueryInterval (implements java.lang.Comparable<T>)
  - htsjdk.samtools.cram.compression.range.RangeCoder
  - htsjdk.samtools.cram.compression.range.RangeDecode
  - htsjdk.samtools.cram.compression.range.RangeEncode
  - htsjdk.samtools.cram.compression.range.RangeParams
  - htsjdk.samtools.cram.compression.rans.RANS4x8Params (implements htsjdk.samtools.cram.compression.rans.RANSParams)
  - htsjdk.samtools.cram.compression.rans.RANSDecode
    - htsjdk.samtools.cram.compression.rans.RANS4x8Decode
    - htsjdk.samtools.cram.compression.rans.RANSNx16Decode
  - htsjdk.samtools.cram.compression.rans.RANSDecodingSymbol
  - htsjdk.samtools.cram.compression.rans.RANSEncode<T>
    - htsjdk.samtools.cram.compression.rans.RANS4x8Encode
    - htsjdk.samtools.cram.compression.rans.RANSNx16Encode
  - htsjdk.samtools.cram.compression.rans.RANSEncodingSymbol
  - htsjdk.samtools.cram.compression.rans.RANSNx16Params (implements htsjdk.samtools.cram.compression.rans.RANSParams)
  - htsjdk.samtools.seekablestream.ReadableSeekableStreamByteChannel (implements java.nio.channels.SeekableByteChannel)
  - htsjdk.samtools.cram.encoding.readfeatures.ReadBase (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    - java.io.BufferedReader
      - java.io.LineNumberReader
        - htsjdk.samtools.util.BufferedLineReader (implements htsjdk.samtools.util.LineReader)
          - htsjdk.samtools.util.StringLineReader
    - htsjdk.tribble.readers.LongLineBufferedReader
  - htsjdk.samtools.filter.ReadNameFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.beta.codecs.reads.ReadsCodecUtils
  - htsjdk.beta.plugin.reads.ReadsDecoderOptions (implements htsjdk.beta.plugin.HtsDecoderOptions)
  - htsjdk.beta.plugin.reads.ReadsEncoderOptions (implements htsjdk.beta.plugin.HtsEncoderOptions)
  - htsjdk.beta.plugin.reads.ReadsFormats
  - htsjdk.samtools.cram.structure.ReadTag (implements java.lang.Comparable<T>)
  - htsjdk.samtools.cram.ref.ReferenceContext (implements java.lang.Comparable<T>)
  - htsjdk.samtools.reference.ReferenceSequence (implements htsjdk.beta.plugin.HtsRecord)
  - htsjdk.samtools.reference.ReferenceSequenceFileFactory
  - htsjdk.samtools.reference.ReferenceSequenceFileWalker (implements java.io.Closeable)
  - htsjdk.samtools.cram.ref.ReferenceSource (implements htsjdk.samtools.cram.ref.CRAMReferenceSource)
  - htsjdk.samtools.cram.encoding.readfeatures.RefSkip (implements htsjdk.samtools.cram.encoding.readfeatures.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.SAMBinaryTagAndValue (implements java.io.Serializable)
    - htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue
  - htsjdk.beta.codecs.reads.sam.SAMCodec (implements htsjdk.beta.plugin.reads.ReadsCodec)
    - htsjdk.beta.codecs.reads.sam.samV1_0.SAMCodecV1_0
  - htsjdk.samtools.util.SamConstants
  - htsjdk.beta.codecs.reads.sam.SAMDecoder (implements htsjdk.beta.plugin.reads.ReadsDecoder)
    - htsjdk.beta.codecs.reads.sam.samV1_0.SAMDecoderV1_0
  - htsjdk.beta.codecs.reads.sam.SAMEncoder (implements htsjdk.beta.plugin.reads.ReadsEncoder)
    - htsjdk.beta.codecs.reads.sam.samV1_0.SAMEncoderV1_0
  - htsjdk.samtools.SAMFileHeader.PgIdGenerator
  - htsjdk.samtools.SamFileHeaderMerger
  - htsjdk.samtools.SamFiles
  - htsjdk.samtools.SAMFileSource
  - htsjdk.samtools.SamFileValidator
  - htsjdk.samtools.SAMFileWriterFactory (implements java.lang.Cloneable)
  - htsjdk.samtools.SAMFileWriterImpl (implements htsjdk.samtools.SAMFileWriter)
    - htsjdk.samtools.BAMFileWriter
    - htsjdk.samtools.CRAMFileWriter
    - htsjdk.samtools.SAMTextWriter
  - htsjdk.samtools.SAMHeaderRecordComparator<T> (implements java.util.Comparator<T>, java.io.Serializable)
  - htsjdk.samtools.SamInputResource
  - htsjdk.samtools.SAMLineParser
  - htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference
  - 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.ReaderImplementation (implements htsjdk.samtools.SamReader.PrimitiveSamReader)
    - htsjdk.samtools.BAMFileReader
    - htsjdk.samtools.CRAMFileReader (implements java.lang.AutoCloseable, htsjdk.samtools.SamReader.Indexing)
    - htsjdk.samtools.HtsgetBAMFileReader
  - htsjdk.samtools.SamReader.Type
  - htsjdk.samtools.SamReaderFactory
  - htsjdk.samtools.SAMRecord (implements java.lang.Cloneable, htsjdk.beta.plugin.HtsRecord, htsjdk.samtools.util.Locatable, java.io.Serializable)
    - htsjdk.samtools.BAMRecord
  - htsjdk.samtools.SAMRecord.SAMTagAndValue
  - htsjdk.samtools.SAMRecordCoordinateComparator (implements htsjdk.samtools.SAMRecordComparator, java.io.Serializable)
  - htsjdk.samtools.SAMRecordDuplicateComparator (implements htsjdk.samtools.SAMRecordComparator, java.io.Serializable)
  - htsjdk.samtools.util.SamRecordIntervalIteratorFactory
  - htsjdk.samtools.util.SAMRecordPrefetchingIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
  - htsjdk.samtools.SAMRecordQueryNameComparator (implements htsjdk.samtools.SAMRecordComparator, java.io.Serializable)
    - htsjdk.samtools.SAMRecordQueryHashComparator (implements java.io.Serializable)
  - htsjdk.samtools.SAMRecordSetBuilder (implements java.lang.Iterable<T>)
  - htsjdk.samtools.util.SamRecordTrackingBuffer<T>
  - htsjdk.samtools.util.SamRecordWithOrdinal
  - htsjdk.samtools.SAMSequenceDictionary (implements htsjdk.beta.plugin.HtsHeader, java.io.Serializable)
  - htsjdk.samtools.SAMSequenceDictionaryCodec
  - htsjdk.variant.utils.SAMSequenceDictionaryExtractor
  - htsjdk.samtools.SAMSortOrderChecker
  - htsjdk.samtools.SamStreams
  - htsjdk.samtools.SAMTagUtil
  - htsjdk.samtools.SAMTestUtil
  - htsjdk.samtools.SAMTextHeaderCodec
  - htsjdk.samtools.SAMUtils
  - htsjdk.samtools.SAMValidationError (implements java.io.Serializable)
  - htsjdk.samtools.SBIIndex (implements java.io.Serializable)
  - htsjdk.samtools.SBIIndex.Header (implements java.io.Serializable)
  - htsjdk.samtools.SBIIndexWriter
  - htsjdk.samtools.cram.encoding.readfeatures.Scores (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - htsjdk.samtools.filter.SecondaryAlignmentFilter (implements htsjdk.samtools.filter.SamRecordFilter)
    - htsjdk.samtools.filter.NotPrimaryAlignmentFilter
  - htsjdk.samtools.SecondaryAlignmentSkippingIterator
    - htsjdk.samtools.NotPrimarySkippingIterator
  - htsjdk.samtools.filter.SecondaryOrSupplementaryFilter (implements htsjdk.samtools.filter.SamRecordFilter)
  - htsjdk.samtools.SecondaryOrSupplementarySkippingIterator
  - htsjdk.samtools.seekablestream.SeekableFTPStreamHelper
  - htsjdk.samtools.seekablestream.SeekableStreamFactory
  - htsjdk.tribble.gff.SequenceRegion (implements htsjdk.samtools.util.Locatable)
  - htsjdk.samtools.util.SequenceUtil
  - htsjdk.variant.variantcontext.SimpleAllele (implements htsjdk.variant.variantcontext.Allele)
  - htsjdk.tribble.bed.SimpleBEDFeature (implements htsjdk.tribble.bed.BEDFeature)
    - htsjdk.tribble.bed.FullBEDFeature (implements htsjdk.tribble.bed.BEDFeature)
  - htsjdk.tribble.SimpleFeature (implements htsjdk.tribble.Feature)
  - htsjdk.samtools.cram.structure.Slice
  - htsjdk.samtools.cram.structure.SliceBlocks
  - htsjdk.samtools.cram.structure.SliceBlocksReadStreams
  - htsjdk.samtools.cram.structure.SliceBlocksWriteStreams
  - htsjdk.samtools.cram.build.SliceFactory
  - htsjdk.samtools.util.SnappyLoader
  - htsjdk.variant.variantcontext.filter.SnpFilter (implements htsjdk.variant.variantcontext.filter.VariantContextFilter)
  - htsjdk.samtools.cram.encoding.readfeatures.SoftClip (implements htsjdk.samtools.cram.encoding.readfeatures.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.StringUtil
  - htsjdk.samtools.cram.encoding.readfeatures.Substitution (implements htsjdk.samtools.cram.encoding.readfeatures.ReadFeature, java.io.Serializable)
  - htsjdk.samtools.cram.structure.SubstitutionMatrix
  - htsjdk.tribble.readers.SynchronousLineReader (implements htsjdk.tribble.readers.LineReader)
  - 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 (implements java.lang.AutoCloseable)
  - 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.cram.structure.TagKeyCache
  - htsjdk.samtools.cram.structure.TagKeyCache.TagKeyInfo
  - htsjdk.samtools.TagValueAndUnsignedArrayFlag
  - htsjdk.samtools.util.TempStreamFactory
  - htsjdk.samtools.util.TestUtil
  - htsjdk.samtools.TextCigarCodec
  - htsjdk.samtools.TextTagCodec
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - java.lang.RuntimeException
        - htsjdk.tribble.exception.CodecLineParsingException
        - htsjdk.samtools.cram.ref.GaveUpException
        - htsjdk.samtools.util.htsget.HtsgetMalformedResponseException
        - htsjdk.beta.exception.HtsjdkException
          - htsjdk.beta.exception.HtsjdkIOException
          - htsjdk.beta.exception.HtsjdkPluginException
            - htsjdk.beta.exception.HtsjdkUnsupportedOperationException
        - htsjdk.samtools.util.RuntimeScriptException
        - htsjdk.samtools.SAMException
          - htsjdk.samtools.cram.CRAMException
          - 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.CorruptedIndexFile
          - 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.samtools.cram.compression.nametokenisation.TokenStreams
  - 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.TrimmingUtil
  - htsjdk.samtools.util.Tuple<A,B>
    - htsjdk.samtools.util.ComparableTuple<A,B> (implements java.lang.Comparable<T>)
  - htsjdk.samtools.cram.build.Utils
  - htsjdk.samtools.cram.compression.rans.Utils
  - htsjdk.utils.ValidationUtils
  - htsjdk.variant.variantcontext.VariantContext (implements htsjdk.tribble.Feature, htsjdk.beta.plugin.HtsRecord, java.io.Serializable)
  - htsjdk.variant.variantcontext.VariantContextBuilder
  - htsjdk.variant.variantcontext.VariantContextComparator (implements java.util.Comparator<T>, java.io.Serializable)
  - htsjdk.variant.variantcontext.VariantContextUtils
  - htsjdk.variant.variantcontext.VariantContextUtils.JexlVCMatchExp
  - htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
  - htsjdk.beta.codecs.variants.vcf.VariantsCodecUtils
  - htsjdk.beta.plugin.variants.VariantsDecoderOptions (implements htsjdk.beta.plugin.HtsDecoderOptions)
  - htsjdk.beta.plugin.variants.VariantsEncoderOptions (implements htsjdk.beta.plugin.HtsEncoderOptions)
  - htsjdk.beta.plugin.variants.VariantsFormats
  - htsjdk.beta.codecs.variants.vcf.VCFCodec (implements htsjdk.beta.plugin.variants.VariantsCodec)
    - htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFCodecV3_2
    - htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFCodecV3_3
    - htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFCodecV4_0
    - htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFCodecV4_1
    - htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFCodecV4_2
    - htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFCodecV4_3
  - htsjdk.variant.vcf.VCFConstants
  - htsjdk.beta.codecs.variants.vcf.VCFDecoder (implements htsjdk.beta.plugin.variants.VariantsDecoder)
    - htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFDecoderV3_2
    - htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFDecoderV3_3
    - htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFDecoderV4_0
    - htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFDecoderV4_1
    - htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFDecoderV4_2
    - htsjdk.beta.codecs.variants.vcf.vcfv4_3.VCFDecoderV4_3
  - htsjdk.beta.codecs.variants.vcf.VCFEncoder (implements htsjdk.beta.plugin.variants.VariantsEncoder)
    - htsjdk.beta.codecs.variants.vcf.vcfv3_2.VCFEncoderV3_2
    - htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFEncoderV3_3
    - htsjdk.beta.codecs.variants.vcf.vcfv4_0.VCFEncoderV4_0
    - htsjdk.beta.codecs.variants.vcf.vcfv4_1.VCFEncoderV4_1
    - htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFEncoderV4_2
  - htsjdk.variant.vcf.VCFEncoder
  - htsjdk.variant.vcf.VCFFileReader (implements htsjdk.variant.vcf.VCFReader)
  - htsjdk.variant.vcf.VCFHeader (implements htsjdk.beta.plugin.HtsHeader, java.io.Serializable)
  - htsjdk.variant.vcf.VCFHeaderLine (implements java.lang.Comparable<T>, java.io.Serializable)
    - 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.VCFAltHeaderLine
      - htsjdk.variant.vcf.VCFContigHeaderLine
      - htsjdk.variant.vcf.VCFFilterHeaderLine
      - htsjdk.variant.vcf.VCFMetaHeaderLine
      - htsjdk.variant.vcf.VCFPedigreeHeaderLine
      - htsjdk.variant.vcf.VCFSampleHeaderLine
  - htsjdk.variant.vcf.VCFHeaderLineTranslator
  - htsjdk.variant.utils.VCFHeaderReader
  - htsjdk.variant.vcf.VCFIteratorBuilder
  - htsjdk.variant.vcf.VCFPassThruTextTransformer (implements htsjdk.variant.vcf.VCFTextTransformer)
  - htsjdk.variant.vcf.VCFPercentEncodedTextTransformer (implements htsjdk.variant.vcf.VCFTextTransformer)
  - htsjdk.variant.vcf.VCFRecordCodec (implements htsjdk.samtools.util.SortingCollection.Codec<T>)
  - htsjdk.variant.vcf.VCFStandardHeaderLines
  - htsjdk.variant.vcf.VCFUtils
  - 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)
  - java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
    - htsjdk.samtools.util.AsciiWriter

## Interface Hierarchy

- java.lang.AutoCloseable
  - java.io.Closeable
    - htsjdk.samtools.BAMIndex
      - htsjdk.samtools.BrowseableBAMIndex
    - htsjdk.samtools.cram.io.BitInputStream
    - htsjdk.samtools.cram.io.BitOutputStream (also extends java.io.Flushable)
    - 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.variant.vcf.VCFIterator
    - htsjdk.samtools.fastq.FastqWriter (also extends htsjdk.io.Writer<A>)
    - htsjdk.tribble.FeatureReader<T>
    - htsjdk.beta.plugin.HtsDecoder<H,R> (also extends htsjdk.beta.plugin.interval.HtsQuery<RECORD>)
      - htsjdk.beta.plugin.hapref.HaploidReferenceDecoder
      - htsjdk.beta.plugin.reads.ReadsDecoder (also extends htsjdk.beta.plugin.reads.ReadsQuery<R>)
      - htsjdk.beta.plugin.variants.VariantsDecoder
    - htsjdk.beta.plugin.HtsEncoder<H,R>
      - htsjdk.beta.plugin.hapref.HaploidReferenceEncoder
      - htsjdk.beta.plugin.reads.ReadsEncoder
      - htsjdk.beta.plugin.variants.VariantsEncoder
    - 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.variant.vcf.VCFReader (also extends java.lang.Iterable<T>)
    - htsjdk.io.Writer<A>
      - htsjdk.samtools.fastq.FastqWriter (also extends java.io.Closeable)
- htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders.Decoder
- htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
- htsjdk.beta.io.bundle.BundleResource
- htsjdk.tribble.index.ChrIndex
- java.lang.Cloneable
  - htsjdk.samtools.SAMFileSpan
  - htsjdk.samtools.util.SortingCollection.Codec<T>
- htsjdk.samtools.util.CollectionUtil.DefaultingMap.Factory<V,K>
- java.lang.Comparable<T>
  - htsjdk.variant.variantcontext.Allele (also extends java.io.Serializable)
- java.util.Comparator<T>
  - htsjdk.samtools.SAMRecordComparator
- htsjdk.samtools.CoordinateSortedPairInfoMap.Codec<KEY,REC>
- htsjdk.samtools.cram.encoding.CRAMCodec<T>
- htsjdk.samtools.CRAMIndexer
- htsjdk.samtools.cram.ref.CRAMReferenceSource
- htsjdk.samtools.CustomReaderFactory.ICustomReaderFactory
- htsjdk.tribble.FeatureCodec<FEATURE_TYPE, SOURCE>
- java.io.Flushable
  - htsjdk.samtools.cram.io.BitOutputStream (also extends java.io.Closeable)
- htsjdk.beta.plugin.HtsDecoderOptions
- htsjdk.beta.plugin.HtsEncoderOptions
- htsjdk.beta.plugin.HtsHeader
- htsjdk.beta.plugin.interval.HtsInterval
- htsjdk.beta.plugin.HtsRecord
- htsjdk.tribble.index.Index
  - htsjdk.tribble.index.MutableIndex
- htsjdk.tribble.index.IndexCreator
- htsjdk.io.IOPath
- htsjdk.samtools.seekablestream.ISeekableStreamFactory
- java.lang.Iterable<T>
  - htsjdk.tribble.CloseableTribbleIterator<T> (also extends htsjdk.samtools.util.CloseableIterator<T>)
  - htsjdk.beta.plugin.interval.HtsQuery<RECORD>
    - htsjdk.beta.plugin.HtsDecoder<H,R> (also extends java.io.Closeable)
      - htsjdk.beta.plugin.hapref.HaploidReferenceDecoder
      - htsjdk.beta.plugin.reads.ReadsDecoder (also extends htsjdk.beta.plugin.reads.ReadsQuery<R>)
      - htsjdk.beta.plugin.variants.VariantsDecoder
  - htsjdk.samtools.SamReader (also extends java.io.Closeable)
  - htsjdk.variant.vcf.VCFReader (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.variant.vcf.VCFIterator
  - htsjdk.tribble.readers.LineIterator
- htsjdk.variant.variantcontext.LazyGenotypesContext.LazyParser
- htsjdk.samtools.util.Locatable
  - htsjdk.tribble.Feature
    - htsjdk.tribble.gff.Gff3Feature
    - htsjdk.tribble.NamedFeature
      - htsjdk.tribble.bed.BEDFeature
- htsjdk.samtools.util.LocationAware
  - htsjdk.tribble.readers.Positional
- htsjdk.samtools.util.Locus
- htsjdk.tribble.NameAwareCodec
- java.util.function.Predicate<T>
  - htsjdk.variant.variantcontext.filter.VariantContextFilter
- htsjdk.samtools.util.ProgressLoggerInterface
- htsjdk.samtools.cram.compression.rans.RANSParams
- htsjdk.samtools.cram.encoding.readfeatures.ReadFeature
- htsjdk.beta.plugin.reads.ReadsQuery<R>
  - htsjdk.beta.plugin.reads.ReadsDecoder (also extends htsjdk.beta.plugin.HtsDecoder<H,R>)
- 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
- java.io.Serializable
  - htsjdk.variant.variantcontext.Allele (also extends java.lang.Comparable<T>)
  - htsjdk.samtools.metrics.Header
- java.util.function.Supplier<T>
  - htsjdk.samtools.util.Lazy.LazyInitializer<T>
- htsjdk.tribble.readers.TabixReader.Iterator
- htsjdk.beta.plugin.Upgradeable
  - htsjdk.beta.plugin.HtsCodec<D,E>
    - htsjdk.beta.plugin.hapref.HaploidReferenceCodec
    - htsjdk.beta.plugin.reads.ReadsCodec
    - htsjdk.beta.plugin.variants.VariantsCodec
- htsjdk.tribble.util.URLHelper
- htsjdk.tribble.util.URLHelperFactory
- htsjdk.samtools.seekablestream.UserPasswordInput
- htsjdk.variant.vcf.VCFIDHeaderLine
- htsjdk.variant.vcf.VCFTextTransformer

## Annotation Interface Hierarchy

- htsjdk.annotations.BetaAPI (implements java.lang.annotation.Annotation)
- htsjdk.annotations.InternalAPI (implements java.lang.annotation.Annotation)

## Enum Class Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    - htsjdk.tribble.index.AbstractIndex.IndexType
    - htsjdk.samtools.util.AbstractRecordAndOffset.AlignmentType
    - htsjdk.samtools.BamIndexValidator.IndexValidationStringency
    - htsjdk.variant.bcf2.BCF2Type
    - htsjdk.tribble.bed.BEDCodec.StartOffset
    - htsjdk.samtools.util.BlockCompressedInputStream.FileTermination
    - htsjdk.samtools.cram.structure.block.BlockCompressionMethod
    - htsjdk.samtools.cram.structure.block.BlockContentType
    - htsjdk.samtools.CigarOperator
    - htsjdk.samtools.cram.digest.ContentDigests.KNOWN_DIGESTS
    - htsjdk.samtools.cram.structure.CRAMCompressionProfile
    - htsjdk.samtools.cram.structure.DataSeries
    - htsjdk.samtools.cram.structure.DataSeriesType
    - htsjdk.samtools.DownsamplingIteratorFactory.Strategy
    - htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy
    - htsjdk.samtools.util.EdgingRecordAndOffset.Type
    - htsjdk.samtools.cram.structure.EncodingID
    - htsjdk.samtools.fastq.FastqConstants.FastqExtensions
    - htsjdk.samtools.util.FastqQualityFormat
    - htsjdk.samtools.fastq.FastqReader.LineType
    - htsjdk.variant.variantcontext.GenotypeType
    - htsjdk.tribble.gff.Gff3Codec.DecodeDepth
    - htsjdk.tribble.gff.Gff3Codec.Gff3Directive
    - htsjdk.samtools.util.GzipCodec.Format
    - htsjdk.beta.plugin.HtsContentType
    - htsjdk.samtools.util.htsget.HtsgetClass
    - htsjdk.samtools.util.htsget.HtsgetFormat
    - htsjdk.samtools.util.htsget.HtsgetRequestField
    - htsjdk.beta.plugin.interval.HtsQueryRule
    - htsjdk.tribble.index.IndexFactory.IndexBalanceApproach
    - htsjdk.tribble.index.IndexFactory.IndexType
    - htsjdk.variant.variantcontext.JexlMissingValueTreatment
    - htsjdk.samtools.util.Log.LogLevel
    - htsjdk.variant.variantcontext.writer.Options
    - htsjdk.samtools.util.QualityEncodingDetector.FileContext
    - htsjdk.samtools.cram.compression.range.RangeParams.ORDER
    - htsjdk.samtools.cram.compression.rans.RANSParams.ORDER
    - htsjdk.samtools.cram.ref.ReferenceContextType
    - htsjdk.samtools.SAMFileHeader.GroupOrder
    - htsjdk.samtools.SAMFileHeader.SortOrder
    - htsjdk.samtools.SAMFlag
    - htsjdk.samtools.SamFlagField
    - htsjdk.samtools.SamIndexes
    - htsjdk.samtools.SamPairUtil.PairOrientation
    - htsjdk.samtools.SamReaderFactory.Option
    - htsjdk.samtools.SAMReadGroupRecord.PlatformValue
    - htsjdk.samtools.SAMTag
    - htsjdk.samtools.SAMValidationError.Severity
    - htsjdk.samtools.SAMValidationError.Type
    - htsjdk.samtools.SQTagUtil.SQBase
    - htsjdk.tribble.annotation.Strand
    - htsjdk.variant.variantcontext.StructuralVariantType
    - htsjdk.samtools.ValidationStringency
    - htsjdk.variant.variantcontext.VariantContext.Type
    - htsjdk.variant.variantcontext.VariantContext.Validation
    - 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

## Record Class Hierarchy

- java.lang.Object
  - java.lang.Record
    - htsjdk.samtools.cram.structure.CompressorDescriptor