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Hierarchy For All Packages
Package Hierarchies:
Accuracy
,
Callers
,
Combiner
,
Exceptions
,
Executable
,
Imputers
,
Utils
,
Utils.Correlation
,
Utils.Distribution
,
Utils.Optimize
,
Utils.Progress
,
Utils.SingleGenotype
,
VCF
,
VCF.Changers
,
VCF.Exceptions
,
VCF.Filters
,
VCF.Mappers
Class Hierarchy
java.lang.Object
Accuracy.
AccuracyCalculator
Accuracy.
AccuracyStats
org.apache.commons.configuration2.event.BaseEventSource (implements org.apache.commons.configuration2.event.EventSource)
org.apache.commons.configuration2.AbstractConfiguration (implements org.apache.commons.configuration2.Configuration)
org.apache.commons.configuration2.AbstractHierarchicalConfiguration<T> (implements java.lang.Cloneable, org.apache.commons.configuration2.HierarchicalConfiguration<T>, org.apache.commons.configuration2.tree.NodeKeyResolver<T>)
org.apache.commons.configuration2.BaseHierarchicalConfiguration (implements java.lang.Cloneable, org.apache.commons.configuration2.tree.InMemoryNodeModelSupport)
org.apache.commons.configuration2.XMLConfiguration (implements org.apache.commons.configuration2.FileBasedConfiguration, org.apache.commons.configuration2.io.FileLocatorAware, org.apache.commons.configuration2.io.InputStreamSupport)
Executable.
ExtendedXMLConfiguration
VCF.
ByteToGeno
Callers.
Caller
Callers.
BiasedBinomialCaller
Callers.
BinomialCaller
Executable.
Case
Executable.
ClassList
<X,Y>
Executable.
CombinerOption
Utils.Distribution.
ComparableDistributionCollector
<V> (implements java.util.stream.Collector<T,A,R>)
Utils.Correlation.
Correlation
Utils.Correlation.
EM
Utils.Correlation.
Pearson
Utils.Distribution.
CountMap
<V>
VCF.Mappers.
DepthMapper
(implements VCF.Mappers.
Mapper
<M>)
Accuracy.
DepthMask
Accuracy.
DepthMaskFactory
Utils.Optimize.
Descent
Utils.Distribution.
Distribution
<V>
Utils.Distribution.
ComparableDistribution
<V>
Utils.Distribution.
DistributionCollector
<V> (implements java.util.stream.Collector<T,A,R>)
Utils.Progress.
DotsProgress
(implements Utils.Progress.
Progress
)
VCF.Mappers.
GenoToByte
(implements VCF.Mappers.
ByteMapper
)
VCF.
Genotype
Utils.Optimize.
GoldenSection
Executable.
ImputationOption
Executable.
Input
Imputers.
KnniLDProb
(implements Imputers.
Imputer
)
Imputers.
KnniLDProbOptimizedCalls
(implements Imputers.
OptimizeImputer
<I>)
Executable.
LinkImputeR
Utils.
Log
Utils.
Matrix
Combiner.
MaxDepthCombiner
(implements Combiner.
Combiner
)
Combiner.
MaxDepthCombinerOptimizedCalls
(implements Combiner.
OptimizeCombiner
<C>)
VCF.Changers.
MaxDepthNoReadsChanger
(implements VCF.Changers.
GenotypeChanger
)
VCF.
Meta
VCF.Changers.
MinDepthMissingChanger
(implements VCF.Changers.
GenotypeChanger
)
Utils.Optimize.
MultipleTest
Executable.
Output
VCF.
Position
VCF.Filters.
PositionFilter
(implements VCF.Filters.
VCFFilter
)
VCF.Filters.
BiallelicFilter
VCF.Filters.
HasDepthFilter
VCF.Filters.
MAFFilter
VCF.Filters.
ParalogHWFilter
VCF.Filters.
PositionMissing
VCF.
PositionMeta
Executable.
PrintStats
Utils.
ProbToCall
Utils.
ProbToCallMinDepth
Utils.Progress.
ProgressFactory
VCF.Changers.
RenameFormatChanger
(implements VCF.Changers.
PositionChanger
)
VCF.
Sample
VCF.Filters.
SampleFilter
(implements VCF.Filters.
VCFFilter
)
VCF.Filters.
SampleMissing
Utils.Progress.
SilentProgress
(implements Utils.Progress.
Progress
)
Utils.SingleGenotype.
SingleGenotypePosition
Utils.SingleGenotype.
SingleGenotypeCall
Utils.SingleGenotype.
SingleGenotypeMasked
Utils.SingleGenotype.
SingleGenotypeProbability
Utils.SingleGenotype.
SingleGenotypeReads
Utils.
SortByIndexDouble
(implements java.util.Comparator<T>)
VCF.Changers.
StandardizeCountsFormatChanger
(implements VCF.Changers.
PositionChanger
)
Utils.Progress.
TextBarProgress
(implements Utils.Progress.
Progress
)
Utils.Progress.
TextProgress
(implements Utils.Progress.
Progress
)
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
Exceptions.
AlgorithmException
Exceptions.
NotEnoughMaskableGenotypesException
Exceptions.
INIException
Exceptions.
OutputException
java.lang.RuntimeException
Exceptions.
ProgrammerException
VCF.Exceptions.
VCFException
VCF.Exceptions.
VCFDataException
VCF.Exceptions.
VCFMissingFormatException
VCF.Exceptions.
VCFNoDataException
VCF.Exceptions.
VCFUnexpectedDataException
VCF.Exceptions.
VCFInputException
VCF.Exceptions.
VCFDataLineException
VCF.Exceptions.
VCFHeaderLineException
Utils.
TopQueue
VCF.
VCF
Interface Hierarchy
VCF.Mappers.
ByteMapper
Combiner.
Combiner
VCF.Mappers.
DoubleMapper
VCF.Changers.
GenotypeChanger
Imputers.
Imputer
VCF.Mappers.
IntegerMapper
VCF.Mappers.
Mapper
<M>
Utils.Optimize.
MultipleIntegerValue
Combiner.
OptimizeCombiner
<C>
Imputers.
OptimizeImputer
<I>
VCF.Changers.
PositionChanger
Utils.Progress.
Progress
Utils.Optimize.
SingleDoubleValue
VCF.Filters.
VCFFilter
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
Accuracy.
AccuracyCalculator.AccuracyMethod
Accuracy.
DepthMask.Method
Utils.
Log.Level
Utils.Progress.
ProgressFactory.ProgressType
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