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Hierarchy For All Packages
Package Hierarchies:
beagleutil
,
blbutil
,
bref
,
haplotype
,
imp
,
ints
,
main
,
math
,
phase
,
sample
,
vcf
Class Hierarchy
java.lang.Object
vcf.
AllData
(implements vcf.
Data
)
bref.
AsIsBref3Writer
(implements bref.
BrefWriter
)
vcf.
BasicGT
(implements vcf.
GT
)
vcf.
BasicMarker
(implements vcf.
Marker
)
vcf.
BasicRefGT
(implements vcf.
RefGT
)
haplotype.
BitHapPair
(implements haplotype.
HapPair
)
vcf.
BitSetGT
(implements vcf.
GTRec
)
bref.
Bref3
bref.
Bref3It
(implements blbutil.
SampleFileIt
<E>)
bref.
Bref3Reader
bref.
BrefBlock
ints.
CharArray
(implements ints.
IntArray
)
beagleutil.
ChromIds
beagleutil.
ChromInterval
(implements java.lang.Comparable<T>, beagleutil.
IntInterval
)
bref.
CompressBref3Writer
(implements bref.
BrefWriter
)
blbutil.
Const
main.
CurrentData
phase.
EstPhase
phase.
EstPhase.HapsGT
(implements vcf.
GT
)
blbutil.
FileUtil
vcf.
FilterUtil
blbutil.
FloatArray
blbutil.
FloatList
imp.
HaplotypeCoder
haplotype.
HapPairPhasedGT
(implements vcf.
GT
)
imp.
ImpData
imp.
ImpIbs
imp.
ImpLS
imp.
ImpLSBaum
imp.
ImpStates
imp.
ImputedRecBuilder
imp.
ImputedVcfWriter
ints.
IndexArray
(implements ints.
IntArray
)
sample.
InitTargHapPairs
blbutil.
InputIt
(implements blbutil.
FileIt
<E>)
vcf.
IntervalVcfIt
<E> (implements blbutil.
SampleFileIt
<E>)
ints.
IntList
ints.
IntMap
<E>
ints.
IntSet
ints.
LongArray
vcf.
LowMafRefDiallelicGT
(implements vcf.
RefGTRec
)
vcf.
LowMafRefGT
(implements vcf.
RefGTRec
)
main.
Main
main.
MainHelper
vcf.
MarkerMap
(implements vcf.
GeneticMap
)
vcf.
Markers
java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
blbutil.
BGZIPOutputStream
ints.
PackedIntArray
(implements ints.
IntArray
)
blbutil.
Pair
<F,S>
main.
Par
main.
Pedigree
phase.
PhaseBaum1
phase.
PhaseData
phase.
PhaseIbs
phase.
PhaseLS
phase.
PhaseStates
vcf.
PlinkGenMap
(implements vcf.
GeneticMap
)
vcf.
PositionMap
(implements vcf.
GeneticMap
)
vcf.
R2Estimator
imp.
RefHapHash
vcf.
RefIt
(implements blbutil.
SampleFileIt
<E>)
math.
Regress
vcf.
RestrictedVcfWindow
(implements java.io.Closeable)
main.
RunStats
beagleutil.
SampleIds
beagleutil.
Samples
vcf.
SeqCodedRefGT
(implements vcf.
RefGTRec
)
bref.
SeqCoder3
vcf.
SplicedGT
(implements vcf.
GT
)
imp.
StateProbsFactory
blbutil.
StringUtil
vcf.
TargetData
(implements vcf.
Data
)
beagleutil.
ThreadSafeIndexer
<T>
bref.
UnBref3
ints.
UnsignedByteArray
(implements ints.
IntArray
)
blbutil.
Utilities
blbutil.
Validate
vcf.
VcfHeader
vcf.
VcfIt
<E> (implements blbutil.
SampleFileIt
<E>)
vcf.
VcfMetaInfo
vcf.
VcfRecBuilder
vcf.
VcfRecGTParser
vcf.
VcfRecord
(implements vcf.
GTRec
)
vcf.
VcfWriter
vcf.
Window
<E>
vcf.
WindowIt
<E> (implements blbutil.
SampleFileIt
<E>)
main.
WindowWriter
(implements java.io.Closeable)
haplotype.
WrappedHapPair
(implements haplotype.
HapPair
)
ints.
WrappedIntArray
(implements ints.
IntArray
)
vcf.
XBasicGT
(implements vcf.
GT
)
vcf.
XBasicGT1
(implements vcf.
XGT1
)
Interface Hierarchy
java.lang.AutoCloseable
java.io.Closeable
bref.
BrefWriter
vcf.
Data
blbutil.
FileIt
<E> (also extends java.util.Iterator<E>)
blbutil.
SampleFileIt
<E>
java.lang.Comparable<T>
vcf.
Marker
blbutil.
Filter
<E>
vcf.
GeneticMap
main.
GenotypeValues
vcf.
GT
vcf.
RefGT
haplotype.
HapPair
ints.
IntArray
vcf.
DuplicatesGTRec
(also extends vcf.
MarkerContainer
)
vcf.
GTRec
vcf.
RefGTRec
beagleutil.
IntInterval
java.util.Iterator<E>
blbutil.
FileIt
<E> (also extends java.io.Closeable)
blbutil.
SampleFileIt
<E>
vcf.
MarkerContainer
vcf.
DuplicatesGTRec
(also extends ints.
IntArray
)
vcf.
GTRec
vcf.
RefGTRec
imp.
StateProbs
vcf.
XGT1
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
beagleutil.
Phase
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