- AllData
- AsIsBref3Writer
- BasicGT
- BasicMarker
- BasicRefGT
- BGZIPOutputStream
- BitHapPair
- BitSetGT
- Bref3
- Bref3It
- Bref3Reader
- BrefBlock
- BrefWriter
- CharArray
- ChromIds
- ChromInterval
- CompressBref3Writer
- Const
- CurrentData
- Data
- DuplicatesGTRec
- EstPhase
- FileIt
- FileUtil
- Filter
- FilterUtil
- FloatArray
- FloatList
- GeneticMap
- GenotypeValues
- GT
- GTRec
- HaplotypeCoder
- HapPair
- HapPairPhasedGT
- ImpData
- ImpIbs
- ImpLS
- ImpLSBaum
- ImpStates
- ImputedRecBuilder
- ImputedVcfWriter
- IndexArray
- InitTargHapPairs
- InputIt
- IntArray
- IntervalVcfIt
- IntInterval
- IntList
- IntMap
- IntSet
- LongArray
- LowMafRefDiallelicGT
- LowMafRefGT
- Main
- MainHelper
- Marker
- MarkerContainer
- MarkerMap
- Markers
- PackedIntArray
- Pair
- Par
- Pedigree
- Phase
- PhaseBaum1
- PhaseData
- PhaseIbs
- PhaseLS
- PhaseStates
- PlinkGenMap
- PositionMap
- R2Estimator
- RefGT
- RefGTRec
- RefHapHash
- RefIt
- Regress
- RestrictedVcfWindow
- RunStats
- SampleFileIt
- SampleIds
- Samples
- SeqCodedRefGT
- SeqCoder3
- SplicedGT
- StateProbs
- StateProbsFactory
- StringUtil
- TargetData
- ThreadSafeIndexer
- UnBref3
- UnsignedByteArray
- Utilities
- Validate
- VcfHeader
- VcfIt
- VcfMetaInfo
- VcfRecBuilder
- VcfRecGTParser
- VcfRecord
- VcfWriter
- Window
- WindowIt
- WindowWriter
- WrappedHapPair
- WrappedIntArray
- XBasicGT
- XBasicGT1
- XGT1