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