Hierarchy For All Packages
Package Hierarchies:- htsjdk.samtools,
- htsjdk.samtools.apps,
- htsjdk.samtools.cram,
- htsjdk.samtools.cram.build,
- htsjdk.samtools.cram.common,
- htsjdk.samtools.cram.compression,
- 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.sra,
- htsjdk.samtools.util,
- htsjdk.samtools.util.ftp,
- 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)
- java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
- java.util.AbstractList<E> (implements java.util.List<E>)
- 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.tribble.bed.BEDCodec
- htsjdk.tribble.IntervalList.IntervalListCodec
- htsjdk.tribble.gff.Gff3Codec
- htsjdk.tribble.AsciiFeatureCodec<T>
- 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>
- java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
- 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
- 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.variant.variantcontext.Allele (implements java.lang.Comparable<T>, java.io.Serializable)
- 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.samtools.cram.BAIEntry (implements java.lang.Comparable<T>)
- 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.BCF2FieldWriter.GenotypesWriter
- 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.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.structure.CompressorCache
- 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.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.CRAMCRAIIndexer (implements htsjdk.samtools.CRAMIndexer)
- 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.encoding.writer.CramRecordWriter
- htsjdk.samtools.cram.build.CRAMReferenceRegion
- 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.Iso8601Date
- 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.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.GZIPExternalCompressor
- htsjdk.samtools.cram.compression.LZMAExternalCompressor
- htsjdk.samtools.cram.compression.RANSExternalCompressor
- htsjdk.samtools.cram.compression.RAWExternalCompressor
- htsjdk.samtools.filter.FailsVendorReadQualityFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- 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.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
- 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.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.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
- 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
- java.io.DataInputStream (implements java.io.DataInput)
- 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.util.BlockCompressedInputStream (implements htsjdk.samtools.util.LocationAware)
- 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.Feature)
- 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.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.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
- 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
- java.util.zip.GZIPOutputStream
- htsjdk.tribble.util.LittleEndianOutputStream
- htsjdk.samtools.util.Md5CalculatingOutputStream
- htsjdk.samtools.util.PositionalOutputStream (implements htsjdk.samtools.util.LocationAware)
- htsjdk.samtools.util.BlockCompressedOutputStream (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.rans.RANS
- 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.samtools.util.BufferedLineReader (implements htsjdk.samtools.util.LineReader)
- java.io.LineNumberReader
- htsjdk.tribble.readers.LongLineBufferedReader
- java.io.BufferedReader
- htsjdk.samtools.filter.ReadNameFilter (implements htsjdk.samtools.filter.SamRecordFilter)
- htsjdk.samtools.cram.structure.ReadTag (implements java.lang.Comparable<T>)
- htsjdk.samtools.sra.ReferenceCache
- htsjdk.samtools.cram.ref.ReferenceContext (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 (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.samtools.util.SamConstants
- 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.SRAFileReader (implements htsjdk.samtools.SamReader.Indexing)
- htsjdk.samtools.SamReader.Type
- htsjdk.samtools.SamReaderFactory
- htsjdk.samtools.SAMRecord (implements java.lang.Cloneable, htsjdk.samtools.util.Locatable, java.io.Serializable)
- htsjdk.samtools.BAMRecord
- htsjdk.samtools.sra.SRALazyRecord
- 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.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 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.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.sra.SRAAccession (implements java.io.Serializable)
- htsjdk.samtools.sra.SRAAlignmentIterator (implements htsjdk.samtools.util.CloseableIterator<T>)
- htsjdk.samtools.SRAIndex (implements htsjdk.samtools.BrowseableBAMIndex)
- htsjdk.samtools.sra.SRAIndexedSequenceFile (implements htsjdk.samtools.reference.ReferenceSequenceFile)
- htsjdk.samtools.SRAIterator (implements htsjdk.samtools.SAMRecordIterator)
- htsjdk.samtools.SRAIterator.RecordRangeInfo
- htsjdk.samtools.sra.SRAUnalignmentIterator (implements java.util.Iterator<E>)
- htsjdk.samtools.sra.SRAUtils
- 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.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.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
- java.lang.RuntimeException
- java.lang.Exception
- 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.TrimmingUtil
- htsjdk.samtools.util.Tuple<A,B>
- htsjdk.samtools.util.ComparableTuple<A,B> (implements java.lang.Comparable<T>)
- htsjdk.samtools.cram.build.Utils
- htsjdk.utils.ValidationUtils
- htsjdk.variant.variantcontext.VariantContext (implements htsjdk.tribble.Feature, 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.variant.vcf.VCFConstants
- htsjdk.variant.vcf.VCFEncoder
- htsjdk.variant.vcf.VCFFileReader (implements htsjdk.variant.vcf.VCFReader)
- htsjdk.variant.vcf.VCFHeader (implements 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.VCFCompoundHeaderLine (implements htsjdk.variant.vcf.VCFIDHeaderLine)
- 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
- htsjdk.samtools.util.AbstractAsyncWriter<T> (implements java.io.Closeable)
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
- 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.variant.vcf.VCFReader (also extends java.lang.Iterable<T>)
- htsjdk.samtools.BAMIndex
- java.io.Closeable
- htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders.Decoder
- htsjdk.samtools.BinningIndexBuilder.FeatureToBeIndexed
- 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.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.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)
- 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.samtools.util.CloseableIterator<T> (also extends java.io.Closeable)
- htsjdk.variant.variantcontext.LazyGenotypesContext.LazyParser
- htsjdk.samtools.util.Locatable
- htsjdk.tribble.Feature
- htsjdk.tribble.bed.BEDFeature
- htsjdk.tribble.gff.Gff3Feature
- htsjdk.tribble.Feature
- 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.encoding.readfeatures.ReadFeature
- 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.samtools.metrics.Header
- java.util.function.Supplier<T>
- htsjdk.samtools.util.Lazy.LazyInitializer<T>
- htsjdk.tribble.readers.TabixReader.Iterator
- htsjdk.tribble.util.URLHelper
- htsjdk.tribble.util.URLHelperFactory
- htsjdk.samtools.seekablestream.UserPasswordInput
- htsjdk.variant.vcf.VCFIDHeaderLine
- htsjdk.variant.vcf.VCFTextTransformer
Enum Hierarchy
- java.lang.Object
- java.lang.Enum<E> (implements java.lang.Comparable<T>, 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.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.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.rans.RANS.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
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)