- AllData
- AlleleImputer
- AsIsBref3Writer
- BasicGT
- BasicMarker
- BestMatch
- BGZIPOutputStream
- BitSetGTRec
- Bref3
- Bref3It
- Bref3Reader
- BrefBlock
- BrefWriter
- CharArray
- ChromIds
- ChromInterval
- CodedSteps
- CodedSteps
- CompHapSegment
- CompressBref3Writer
- Const
- Data
- DoubleArray
- DuplicatesGTRec
- EstPhase
- FileIt
- FileUtil
- Filter
- FilterUtil
- FixedPhaseData
- FloatArray
- FloatList
- FwdBwd
- GeneticMap
- GT
- GTRec
- HapImputer
- HaplotypeCoder
- HapsGT
- HmmUpdater
- Ibs2
- ImpData
- ImpIbs
- ImpLS
- ImpLSBaum
- ImpStates
- ImputeBaum
- ImputedRecBuilder
- ImputedVcfWriter
- IndexArray
- InputIt
- IntArray
- IntervalVcfIt
- IntInterval
- IntIntMap
- IntList
- LongArray
- LowFreqPhaseIbs
- LowMafRefDiallelicGTRec
- LowMafRefGTRec
- Main
- MainHelper
- Marker
- MarkerContainer
- MarkerIndices
- MarkerMap
- Markers
- MultiThreadUtils
- PackedIntArray
- Pair
- Par
- PbwtPhaseIbs
- PbwtUpdater
- Pedigree
- PhaseBaum1
- PhaseData
- PhaseIbs
- PhaseLS
- PhaseStates
- PlinkGenMap
- PositionMap
- RecombRegress
- RefGT
- RefGTRec
- RefHapHash
- RefIt
- Regress
- RestrictedGT
- RestrictedVcfWindow
- RunStats
- SampleFileIt
- SampleIds
- Samples
- SampleSeg
- SeqCodedRefGTRec
- SeqCoder3
- SplicedGT
- StateProbs
- StateProbsFactory
- StringUtil
- TargetData
- ThreadSafeIndexer
- UnBref3
- UnsignedByteArray
- Utilities
- Validate
- VcfHeader
- VcfIt
- VcfMetaInfo
- VcfRec
- VcfRecBuilder
- VcfRecGTParser
- VcfWriter
- Window
- WindowIt
- WindowWriter
- WrappedIntArray