All Classes
AL
AllData
AlleleProbs
BasicAlleleProbs
BasicGenotypeValues
BasicGL
BasicHapPairs
BasicIntInterval
BasicMarker
BasicSampleHapPairs
BGZIPOutputStream
BitHapPair
BitSetGT
BitSetRefGT
Bref
BrefIt
ByteArrayRefGT
ByteIndexArray
CenteredIntIntervalTree
CharIndexArray
ChromIds
ChromInterval
ConsensusPhaser
Const
ConstrainedAlleleProbs
ConsumeSingleSamples
CurrentData
Dag
DagLevel
DagUtil
Data
DiploidStates
DuoBaumLevel
DuoNodes
FileIt
FileUtil
Filter
FilterUtil
FuzzyGL
GeneticMap
GenotypeCorrection
GenotypeValues
GL
GLSampleHapPairs
GprobsStatistics
HapAlleleProbs
HapBaumLevel
HaploidIbd
Haplotype
HaplotypeCoder
HapNodes
HapPair
HapPairs
HapPairSampler
HapSegment
HapsMarker
HapsMarkerIterator
HbdAL
HighCapacityDagLevel
IbdBaum
IbdSegment
IbsHapSegments
ImmutableDag
ImputationData
IndexMap
IndexSet
InputIt
IntArray
IntervalVcfIt
IntInterval
IntIntervalTree
IntList
IntPair
IntSet
LiAndStephensHapSampler
LinkageEquilibriumDag
LowCapacityDagLevel
LowMafRefDiallelicGT
LowMafRefGT
LowMemHapAlleleProbs
LSHapBaum
Main
MainHelper
Marker
MarkerContainer
Markers
MaskedEndsGL
MergeableDag
MergeableDagLevel
NoPhaseGL
NuclearFamilies
Par
Phase
PlinkGeneticMap
PositionMap
R2Estimator
RecombHapPairSampler
RecombSingleBaum
RecombSingleBaumLevel
RecombSingleNodes
RefGL
RefHapPairs
RefHapSeg
RefHapSegs
RefIt
RestrictedDag
RestrictedVcfWindow
RevGenotypeValues
RevGL
RevHapPair
RevHapPairs
RevSampleHapPairs
RunStats
SampleFileIt
SampleGenotypeValues
SampleHapPairAlleleProbs
SampleHapPairs
SampleIds
SamplerData
Samples
Score
SeqCodedRefGT
ShiftedByteIndexArray
SingleBaum
SingleBaumInterface
SingleBaumLevel
SingleNodes
SplicedGL
StringUtil
TargetData
ThreadSafeIndexer
Utilities
Validate
VcfEmission
VcfEmissionCompressor
VcfHeader
VcfIt
VcfMetaInfo
VcfRecBuilder
VcfRecGTParser
VcfRecord
VcfWindow
VcfWriter
Weights
WindowWriter
WrappedHapPair
WrappedIntArray