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Hierarchy For All Packages
Package Hierarchies:
beagleutil
,
blbutil
,
dag
,
haplotype
,
ibd
,
main
,
sample
,
vcf
Class Hierarchy
java.lang.Object
vcf.
AllData
(implements vcf.
Data
)
main.
BasicAlleleProbs
(implements main.
AlleleProbs
)
main.
BasicGenotypeValues
(implements main.
GenotypeValues
)
vcf.
BasicGL
(implements vcf.
GL
)
haplotype.
BasicHapPairs
(implements haplotype.
HapPairs
)
beagleutil.
BasicIntInterval
(implements java.lang.Comparable<T>, beagleutil.
IntInterval
)
vcf.
BasicMarker
(implements vcf.
Marker
)
haplotype.
BasicSampleHapPairs
(implements haplotype.
SampleHapPairs
)
haplotype.
BitHapPair
(implements haplotype.
HapPair
)
vcf.
BitSetGT
(implements vcf.
VcfEmission
)
vcf.
BitSetRefGT
(implements vcf.
VcfEmission
)
vcf.
Bref
vcf.
BrefIt
(implements blbutil.
SampleFileIt
<E>)
vcf.
ByteArrayRefGT
(implements vcf.
VcfEmission
)
blbutil.
ByteIndexArray
(implements blbutil.
IntArray
)
beagleutil.
CenteredIntIntervalTree
<E> (implements beagleutil.
IntIntervalTree
<E>)
blbutil.
CharIndexArray
(implements blbutil.
IntArray
)
beagleutil.
ChromIds
beagleutil.
ChromInterval
(implements java.lang.Comparable<T>, beagleutil.
IntInterval
)
haplotype.
ConsensusPhaser
blbutil.
Const
main.
ConstrainedAlleleProbs
(implements main.
AlleleProbs
)
sample.
ConsumeSingleSamples
(implements java.lang.Runnable)
main.
CurrentData
dag.
DagUtil
sample.
DuoBaumLevel
sample.
DuoNodes
blbutil.
FileUtil
vcf.
FilterUtil
vcf.
FuzzyGL
(implements vcf.
GL
)
haplotype.
GenotypeCorrection
haplotype.
GLSampleHapPairs
(implements haplotype.
SampleHapPairs
)
vcf.
GprobsStatistics
sample.
HapBaumLevel
ibd.
HaploidIbd
ibd.
Haplotype
sample.
HaplotypeCoder
sample.
HapNodes
main.
HapPairSampler
ibd.
HapSegment
(implements java.lang.Comparable<T>, beagleutil.
IntInterval
)
haplotype.
HapsMarkerIterator
(implements blbutil.
FileIt
<E>)
vcf.
HbdAL
(implements vcf.
AL
)
dag.
HighCapacityDagLevel
(implements dag.
DagLevel
)
ibd.
IbdBaum
ibd.
IbdSegment
ibd.
IbsHapSegments
dag.
ImmutableDag
(implements dag.
Dag
)
sample.
ImputationData
blbutil.
IndexMap
blbutil.
IndexSet
blbutil.
InputIt
(implements blbutil.
FileIt
<E>)
vcf.
IntervalVcfIt
<E> (implements blbutil.
SampleFileIt
<E>)
blbutil.
IntList
blbutil.
IntPair
(implements java.lang.Comparable<T>)
blbutil.
IntSet
main.
LiAndStephensHapSampler
dag.
LinkageEquilibriumDag
(implements dag.
Dag
)
dag.
LowCapacityDagLevel
(implements dag.
DagLevel
)
vcf.
LowMafRefDiallelicGT
(implements vcf.
VcfEmission
)
vcf.
LowMafRefGT
(implements vcf.
VcfEmission
)
main.
LowMemHapAlleleProbs
(implements main.
HapAlleleProbs
)
sample.
LSHapBaum
main.
Main
main.
MainHelper
vcf.
Markers
vcf.
MaskedEndsGL
(implements vcf.
GL
)
dag.
MergeableDag
dag.
MergeableDagLevel
vcf.
NoPhaseGL
(implements vcf.
GL
)
main.
NuclearFamilies
java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
blbutil.
BGZIPOutputStream
main.
Par
main.
PlinkGeneticMap
(implements main.
GeneticMap
)
main.
PositionMap
(implements main.
GeneticMap
)
vcf.
R2Estimator
main.
RecombHapPairSampler
sample.
RecombSingleBaum
(implements sample.
SingleBaumInterface
)
sample.
RecombSingleBaumLevel
sample.
RecombSingleNodes
vcf.
RefGL
(implements vcf.
GL
)
haplotype.
RefHapPairs
(implements haplotype.
SampleHapPairs
)
sample.
RefHapSeg
sample.
RefHapSegs
vcf.
RefIt
(implements blbutil.
SampleFileIt
<E>)
sample.
RestrictedDag
vcf.
RestrictedVcfWindow
(implements java.io.Closeable)
main.
RevGenotypeValues
(implements main.
GenotypeValues
)
vcf.
RevGL
(implements vcf.
GL
)
haplotype.
RevHapPair
(implements haplotype.
HapPair
)
haplotype.
RevHapPairs
(implements haplotype.
HapPairs
)
haplotype.
RevSampleHapPairs
(implements haplotype.
SampleHapPairs
)
main.
RunStats
main.
SampleGenotypeValues
main.
SampleHapPairAlleleProbs
(implements main.
AlleleProbs
)
beagleutil.
SampleIds
sample.
SamplerData
beagleutil.
Samples
dag.
Score
(implements java.lang.Comparable<T>)
vcf.
SeqCodedRefGT
(implements vcf.
VcfEmission
)
blbutil.
ShiftedByteIndexArray
(implements blbutil.
IntArray
)
sample.
SingleBaum
(implements sample.
SingleBaumInterface
)
sample.
SingleBaumLevel
sample.
SingleNodes
vcf.
SplicedGL
(implements vcf.
GL
)
blbutil.
StringUtil
vcf.
TargetData
(implements vcf.
Data
)
beagleutil.
ThreadSafeIndexer
<T>
blbutil.
Utilities
blbutil.
Validate
vcf.
VcfEmissionCompressor
vcf.
VcfHeader
vcf.
VcfIt
<E> (implements blbutil.
SampleFileIt
<E>)
vcf.
VcfMetaInfo
vcf.
VcfRecBuilder
vcf.
VcfRecGTParser
vcf.
VcfRecord
(implements vcf.
VcfEmission
)
vcf.
VcfWindow
(implements java.io.Closeable)
vcf.
VcfWriter
haplotype.
Weights
main.
WindowWriter
(implements java.io.Closeable)
haplotype.
WrappedHapPair
(implements haplotype.
HapPair
)
blbutil.
WrappedIntArray
(implements blbutil.
IntArray
)
Interface Hierarchy
vcf.
AL
main.
AlleleProbs
java.lang.AutoCloseable
java.io.Closeable
vcf.
Data
blbutil.
FileIt
<E> (also extends java.util.Iterator<E>)
blbutil.
SampleFileIt
<E>
java.lang.Comparable<T>
vcf.
Marker
dag.
Dag
dag.
DagLevel
sample.
DiploidStates
blbutil.
Filter
<E>
main.
GeneticMap
main.
GenotypeValues
vcf.
GL
main.
HapAlleleProbs
haplotype.
HapPair
haplotype.
HapPairs
haplotype.
SampleHapPairs
blbutil.
IntArray
beagleutil.
IntInterval
beagleutil.
IntIntervalTree
<E>
java.util.Iterator<E>
blbutil.
FileIt
<E> (also extends java.io.Closeable)
blbutil.
SampleFileIt
<E>
vcf.
MarkerContainer
vcf.
HapsMarker
vcf.
VcfEmission
vcf.
VcfEmission
sample.
SingleBaumInterface
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
beagleutil.
Phase
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