All Classes
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