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genoAccuracy(byte) - Method in class Accuracy.AccuracyStats
Return the accuracy for a given genotype
genoCorrect(byte) - Method in class Accuracy.AccuracyStats
Return the number of genotypes that are correct that have the give true genotype
GenoToByte - Class in VCF.Mappers
Maps from a text string representing a genotype to a byte representing a genotype
GenoToByte() - Constructor for class VCF.Mappers.GenoToByte
Default constructor
genoTotal(byte) - Method in class Accuracy.AccuracyStats
Return the number of genotypes used in the accuracy calculation that have the give true genotype
Genotype - Class in VCF
Represents a single genotype in a VCF file
GenotypeChanger - Interface in VCF.Changers
Changes a genotype
genotypeList() - Method in class VCF.Position
Get a list of genotypes for this position
genotypeList() - Method in class VCF.Sample
Get a list of genotypes for this sample
genotypesByPositionStream() - Method in class VCF.VCF
Gets a stream of genotypes by position.
genotypesBySampleStream() - Method in class VCF.VCF
Gets a stream of genotypes by sample.
genotypeStream() - Method in class VCF.Position
Get a stream of genotypes for this position
genotypeStream() - Method in class VCF.Sample
Get a stream of genotypes for this sample
genotypeStream() - Method in class VCF.VCF
Gets a stream of genotypes.
get(long) - Static method in class Utils.Progress.ProgressFactory
Get a new instance
get(String, X) - Method in class Executable.ClassList
Get a new instance of the child class
get(V) - Method in class Utils.Distribution.CountMap
Get the count of the given object
get2DArray(int) - Method in class VCF.Mappers.DepthMapper
 
get2DArray(int) - Method in interface VCF.Mappers.Mapper
Get a 2d array of the returned type
getAdditional() - Method in class Executable.Case
Get the additional information for this case
getAlt() - Method in class VCF.PositionMeta
Get the alternative alleles
getArray(int) - Method in class VCF.Mappers.DepthMapper
 
getArray(int) - Method in interface VCF.Mappers.Mapper
Get an array of the returned type
getCall() - Method in class Utils.SingleGenotype.SingleGenotypeCall
Get the call
getCaller() - Method in class Executable.Case
Get the caller for this case
getCaller() - Method in class Utils.MAFCalculator
Gets the caller used in the MAF calculation
getCaller(HierarchicalConfiguration<ImmutableNode>) - Static method in class Executable.Available
Returns the caller for the given configuration
getChrom() - Method in class VCF.PositionMeta
Get the chromosome
getCombiner() - Method in class Executable.Case
Get the combiner for this case if it doesn't require optimizing, else throw an error
getCombiner() - Method in class Executable.CombinerOption
Returns the combiner if the combiner option was for a non-optimizable combiner, else throws an exception
getCombiner(List<SingleGenotypeProbability>, List<SingleGenotypeProbability>, List<SingleGenotypeReads>, List<SingleGenotypeCall>, List<SingleGenotypeMasked>) - Method in class Executable.Case
Get the combiner for this case.
getCombiner(List<SingleGenotypeProbability>, List<SingleGenotypeProbability>, List<SingleGenotypeReads>, List<SingleGenotypeCall>, List<SingleGenotypeMasked>) - Method in class Executable.CombinerOption
Gets a combiner.
getConfig() - Method in class Accuracy.DepthMaskFactory
Get the config for the factory
getConfig() - Method in class Callers.BiasedBinomialCaller
 
getConfig() - Method in class Callers.BinomialCaller
 
getConfig() - Method in class Callers.Caller
Get the config for the caller
getConfig() - Method in class Callers.LogBiasedBinomialCaller
 
getConfig() - Method in class Callers.LogBinomialCaller
 
getConfig() - Method in interface Combiner.Combiner
Get the config for the caller
getConfig() - Method in class Combiner.MaxDepthCombiner
 
getConfig() - Method in class Combiner.MaxDepthCombinerOptimizedCalls
 
getConfig() - Method in interface Combiner.OptimizeCombiner
Get the config for the optimizable combiner
getConfig() - Method in class Executable.Case
Get the config for this case
getConfig() - Method in class Executable.CombinerOption
Get the combiner options config
getConfig() - Method in class Executable.ImputationOption
Get the imputer options config
getConfig() - Method in class Executable.Input
Get the input config
getConfig() - Method in class Executable.Output
Get the input config for the final imputation step
getConfig() - Method in class Executable.PrintStats
Get the imputer options config
getConfig() - Method in interface Imputers.Imputer
Get the config for the imputer
getConfig() - Method in class Imputers.KnniLDProb
 
getConfig() - Method in class Imputers.KnniLDProbOptimizedCalls
 
getConfig() - Method in interface Imputers.OptimizeImputer
Get the config for this case
getConfig() - Method in class VCF.Filters.BiallelicFilter
 
getConfig() - Method in class VCF.Filters.HasDepthFilter
 
getConfig() - Method in class VCF.Filters.MAFFilter
 
getConfig() - Method in class VCF.Filters.ParalogHWFilter
 
getConfig() - Method in class VCF.Filters.PositionMissing
 
getConfig() - Method in class VCF.Filters.SampleMissing
 
getConfig() - Method in interface VCF.Filters.VCFFilter
Get the config for this filter
getConfig(Log.Level, File) - Static method in class Utils.Log
Get the config for a caller
getCount(V) - Method in class Utils.Distribution.Distribution
Get the count for an object
getData() - Method in class VCF.Genotype
Get all the data associated with this genotype
getData(String) - Method in class VCF.Genotype
Get a specified piece of data for this genotype.
getDepthMask(int[][][], Caller) - Method in class Accuracy.DepthMaskFactory
Get a depth mask
getDepthMask(int[][][], List<SingleGenotypePosition>, Caller) - Method in class Accuracy.DepthMaskFactory
Get a depth mask
getError() - Method in class Callers.BiasedBinomialCaller
Get the eror rate used in the caller
getError() - Method in class Callers.LogBiasedBinomialCaller
Get the eror rate used in the caller
getFilter() - Method in class VCF.PositionMeta
Get the filters
getFilter(HierarchicalConfiguration<ImmutableNode>) - Static method in class Executable.Available
Returns the VCF filter for the given configuration
getFilterSummary() - Method in class Executable.Case
Get a summary of filters used in this case
getFormat() - Method in class VCF.PositionMeta
Get a list of formats
getID() - Method in class VCF.PositionMeta
Get the ID
getImputeConfig() - Method in class Executable.Input
Get the input config for the final imputation step
getImputeConfig(Caller, Imputer, Combiner) - Method in class Executable.Case
Get the final imputation stage config for this case
getImputer() - Method in class Executable.Case
Get the imputer for this case if it doesn't require optimizing, else throw an error
getImputer() - Method in class Executable.ImputationOption
Returns the imputer if the imputer option was for a non-optimizable imputer, else throws an exception
getImputer(double[][][], int[][][], List<SingleGenotypeProbability>, List<SingleGenotypeMasked>) - Method in class Executable.Case
Get the imputer for this case.
getImputer(double[][][], int[][][], List<SingleGenotypeProbability>, List<SingleGenotypeMasked>) - Method in class Executable.ImputationOption
Gets an imputer.
getInfo() - Method in class VCF.PositionMeta
Get the info
getLinesList() - Method in class VCF.Meta
Get the meta lines
getLinesStream() - Method in class VCF.Meta
Get the meta lines
getList() - Method in class Utils.TopQueue
Returns the entries in the queue as an array
getList(int) - Method in class Utils.TopQueue
Returns the entries in the queue as an array.
getMaf() - Method in class Utils.SingleGenotype.SingleGenotypeMasked
Get the minor allele frequency for the position of this genotypes
getMasked() - Method in class Utils.SingleGenotype.SingleGenotypeMasked
Get the masked read counts
getMaskedDepth() - Method in class Utils.SingleGenotype.SingleGenotypeMasked
Get the masked depth
getMaxDepth() - Method in class Accuracy.AccuracyStats
Gte the maximum depth (read count) of any genotype used in the accuracy calculation
getMaxDepth() - Method in class Utils.MAFCalculator
Gets the maximum depth used in the MAF calculation
getMeta() - Method in class VCF.VCF
Get the meta information for this VCF
getMinDepth() - Method in class Utils.MAFCalculator
Gets the minimum depth used in the MAF calculation
getName() - Method in class Executable.Case
Get the name of this case
getOptimized(double[][][], int[][][], List<SingleGenotypeProbability>, List<SingleGenotypeMasked>) - Method in class Imputers.KnniLDProbOptimizedCalls
 
getOptimized(double[][][], int[][][], List<SingleGenotypeProbability>, List<SingleGenotypeMasked>) - Method in interface Imputers.OptimizeImputer
Get an optimized version of the imputer
getOptimized(List<SingleGenotypeProbability>, List<SingleGenotypeProbability>, List<SingleGenotypeReads>, List<SingleGenotypeCall>, List<SingleGenotypeMasked>) - Method in class Combiner.MaxDepthCombinerOptimizedCalls
 
getOptimized(List<SingleGenotypeProbability>, List<SingleGenotypeProbability>, List<SingleGenotypeReads>, List<SingleGenotypeCall>, List<SingleGenotypeMasked>) - Method in interface Combiner.OptimizeCombiner
Returns an optimized combiner for the given inputs
getOriginal() - Method in class Utils.SingleGenotype.SingleGenotypeMasked
Get the original read counts
getPartial() - Method in class Executable.Output
Should we write partial output
getPosition() - Method in class VCF.PositionMeta
Get the position (within a chromosome) of the position
getPositionFilter(HierarchicalConfiguration<ImmutableNode>) - Static method in class Executable.Available
Returns the Position filter for the given configuration
getPositionMeta() - Method in class VCF.Genotype
Get the position metadata for the position associated with this genotype
getPositions() - Method in class VCF.VCF
Get a stream of position meta data
getPrintStats() - Method in class Executable.Case
Get the PrintStats object for this case
getProb() - Method in class Utils.SingleGenotype.SingleGenotypeProbability
Get the genotype probabilities
getProportion(V) - Method in class Utils.Distribution.Distribution
Get the proportion for n object.
getQual() - Method in class VCF.PositionMeta
Get the quality
getReads() - Method in class Utils.SingleGenotype.SingleGenotypeReads
Gets the reads
getRef() - Method in class VCF.PositionMeta
Get the reference allele
getSample() - Method in class Utils.SingleGenotype.SingleGenotypePosition
Get the sample position
getSampleName() - Method in class VCF.Genotype
Get the sample name for the name associated with this genotype
getSamples() - Method in class VCF.VCF
Get a stream of sample names
getSNP() - Method in class Utils.SingleGenotype.SingleGenotypePosition
Get the snp position
getSummary() - Method in class VCF.Filters.BiallelicFilter
 
getSummary() - Method in class VCF.Filters.HasDepthFilter
 
getSummary() - Method in class VCF.Filters.MAFFilter
 
getSummary() - Method in class VCF.Filters.ParalogHWFilter
 
getSummary() - Method in class VCF.Filters.PositionMissing
 
getSummary() - Method in class VCF.Filters.SampleMissing
 
getSummary() - Method in interface VCF.Filters.VCFFilter
Gets a string summary of this filter
getSummaryWriter() - Method in class Executable.Output
Gets the writer to write summary information to
getTableWriter() - Method in class Executable.Output
Gets the writer to write table information to
getTotal() - Method in class Utils.Distribution.Distribution
Get the total count for all objects
getValueList() - Method in class Utils.TopQueue
Returns the entries in the values as an array
getValueList(int) - Method in class Utils.TopQueue
Returns the values in the queue as an array.
getVCF() - Method in class Executable.Input
Get the VCF data
GoldenSection - Class in Utils.Optimize
Optimizes the input to a function of type SingleDoubleValue using the Golden Section method
GoldenSection(double, double) - Constructor for class Utils.Optimize.GoldenSection
Constructor
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