Hierarchy For All Packages

Package Hierarchies:

• beagleutil,
• blbutil,
• bref,
• imp,
• ints,
• main,
• phase,
• vcf

Class Hierarchy

• java.lang.Object
  • bref.AsIsBref3Writer (implements bref.BrefWriter)
  • vcf.BasicGT (implements vcf.GT)
  • vcf.BasicGTRec (implements vcf.GTRec)
  • vcf.BasicMarker (implements vcf.Marker)
  • phase.BasicPhaseStates
  • blbutil.BitArray
  • vcf.BitArrayGTRec (implements vcf.GTRec)
  • vcf.BitArrayRefGTRec (implements vcf.GTRec)
  • blbutil.BlockLineReader (implements blbutil.FileIt<E>)
  • bref.Bref3
  • bref.Bref3It (implements blbutil.SampleFileIt<E>)
  • bref.Bref3Reader
  • bref.BrefBlock
  • ints.CharArray (implements ints.IntArray)
  • beagleutil.ChromIds
  • beagleutil.ChromInterval (implements java.lang.Comparable<T>, beagleutil.IntInterval)
  • imp.CodedSteps
  • phase.CodedSteps
  • beagleutil.CompHapSegment (implements java.lang.Comparable<T>)
  • bref.CompressBref3Writer (implements bref.BrefWriter)
  • blbutil.Const
  • blbutil.DoubleArray
  • phase.EstPhase
  • blbutil.FileUtil
  • vcf.FilterUtil
  • phase.FixedPhaseData
  • blbutil.FloatArray
  • blbutil.FloatList
  • phase.FwdPbwtPhaser
  • imp.HaplotypeCoder
  • phase.HmmParamData
  • phase.HmmStateProbs
  • phase.HmmUpdater
  • phase.Ibs2
  • phase.Ibs2Markers
  • phase.Ibs2Sets
  • imp.ImpData
  • imp.ImpIbs
  • imp.ImpLS
  • imp.ImpLSBaum
  • imp.ImpStates
  • imp.ImputedRecBuilder
  • imp.ImputedVcfWriter
  • ints.IndexArray (implements ints.IntArray)
  • blbutil.InputIt (implements blbutil.FileIt<E>)
  • vcf.IntervalVcfIt<E> (implements blbutil.SampleFileIt<E>)
  • ints.IntIntMap
  • ints.IntList
  • phase.LowFreqPbwtPhaseIbs
  • phase.LowFreqPhaseIbs
  • phase.LowFreqPhaseStates
  • vcf.LowMafDiallelicGTRec (implements vcf.GTRec)
  • vcf.LowMafGTRec (implements vcf.GTRec)
  • vcf.LowMafRefDiallelicGTRec (implements vcf.RefGTRec)
  • vcf.LowMafRefGTRec (implements vcf.RefGTRec)
  • main.Main
  • phase.MarkerCluster
  • vcf.MarkerIndices
  • vcf.MarkerMap
  • vcf.Markers
  • blbutil.MultiThreadUtils
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • blbutil.BGZIPOutputStream
  • ints.PackedIntArray (implements ints.IntArray)
  • main.Par
  • phase.ParamEstimates
  • beagleutil.PbwtDivUpdater
  • phase.PbwtIbsData
  • phase.PbwtPhaseIbs
  • phase.PbwtPhaser
  • phase.PbwtRecPhaser
  • beagleutil.PbwtUpdater
  • main.Pedigree
  • phase.PhaseBaum1
  • phase.PhaseData
  • phase.PhaseLS
  • vcf.PlinkGenMap (implements vcf.GeneticMap)
  • vcf.PositionMap (implements vcf.GeneticMap)
  • vcf.RefGT (implements vcf.GT)
  • imp.RefHapHash
  • vcf.RefIt (implements blbutil.SampleFileIt<E>)
  • vcf.RefTargSlidingWindow (implements vcf.SlidingWindow)
  • vcf.RestrictedGT (implements vcf.GT)
  • vcf.RestrictedVcfWindow (implements java.io.Closeable)
  • phase.RevPbwtPhaser
  • main.RunStats
  • beagleutil.SampleIds
  • phase.SamplePhase
  • vcf.Samples
  • phase.SampleSeg (implements java.lang.Comparable<T>, beagleutil.IntInterval)
  • vcf.SeqCodedRefGTRec (implements vcf.RefGTRec)
  • bref.SeqCoder3
  • vcf.SplicedGT (implements vcf.GT)
  • phase.Stage2Baum
  • phase.Stage2Haps
  • imp.StateProbsFactory
  • vcf.Steps
  • blbutil.StringUtil
  • ints.SynchedIntList
  • vcf.TargSlidingWindow (implements vcf.SlidingWindow)
  • beagleutil.ThreadSafeIndexer<T>
  • bref.UnBref3
  • ints.UnsignedByteArray (implements ints.IntArray)
  • blbutil.Utilities
  • blbutil.Validate
  • vcf.VcfHeader
  • vcf.VcfIt<E> (implements blbutil.SampleFileIt<E>)
  • vcf.VcfMetaInfo
  • vcf.VcfRec (implements vcf.GTRec)
  • vcf.VcfRecBuilder
  • vcf.VcfRecGTParser
  • vcf.VcfRecGTParser.HapListRep
  • vcf.VcfWriter
  • vcf.Window
  • main.WindowWriter (implements java.io.Closeable)
  • ints.WrappedIntArray (implements ints.IntArray)
  • vcf.XRefGT (implements vcf.GT)

Interface Hierarchy

• java.lang.AutoCloseable
  • java.io.Closeable
    • bref.BrefWriter
    • blbutil.FileIt<E> (also extends java.util.Iterator<E>)
      • blbutil.SampleFileIt<E>
    • vcf.SlidingWindow
• java.lang.Comparable<T>
  • vcf.Marker
• blbutil.Filter<E>
• vcf.GeneticMap
• vcf.GT
• ints.IntArray
  • vcf.DuplicatesGTRec (also extends vcf.MarkerContainer)
    • vcf.GTRec
      • vcf.RefGTRec
• beagleutil.IntInterval
• java.util.Iterator<E>
  • blbutil.FileIt<E> (also extends java.io.Closeable)
    • blbutil.SampleFileIt<E>
• vcf.MarkerContainer
  • vcf.DuplicatesGTRec (also extends ints.IntArray)
    • vcf.GTRec
      • vcf.RefGTRec
• imp.StateProbs