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