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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C
- calculate(byte[][]) - Method in class Utils.Correlation.Correlation
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Calculates correlations between all pairs of arrays
- calculate(byte[], byte[]) - Method in class Utils.Correlation.Correlation
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Calculates the correlation between two arrays
- calculate(byte[], byte[]) - Method in class Utils.Correlation.EM
- calculate(byte[], byte[]) - Method in class Utils.Correlation.Pearson
- call(double[][][]) - Method in class Utils.ProbToCall
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Call a table of genotypes
- call(double[][][], int[][][]) - Method in class Utils.ProbToCallMinDepth
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Call a table of genotypes
- call(int[][][]) - Method in class Callers.Caller
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Calls genotypes for every genotype
- call(List<SingleGenotypeProbability>) - Method in class Utils.ProbToCall
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Call a list of genotypes
- call(List<SingleGenotypeReads>) - Method in class Callers.Caller
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Call the selected genotypes
- Caller - Class in Callers
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Represents a genotype caller
- Caller() - Constructor for class Callers.Caller
- Callers - package Callers
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Provides classes for calculating called genotype probabilities.
- callSingle(double[]) - Method in class Utils.ProbToCall
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Call a single genotype
- callSingle(double[], int[]) - Method in class Utils.ProbToCallMinDepth
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Call a single genotype
- callSingle(int[]) - Method in class Callers.BiasedBinomialCaller
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Calls a genotype based on reads
- callSingle(int[]) - Method in class Callers.Caller
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Call a single genotype
- callSingle(int[]) - Method in class Callers.LogBiasedBinomialCaller
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Calls a genotype based on reads
- Case - Class in Executable
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Represent the LinkImputeR inputs for a single case (filters, caller, imputer and combiner)
- Case(String, List<VCFFilter>, Caller, ImputationOption, CombinerOption, PrintStats, String) - Constructor for class Executable.Case
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Constructor
- Case(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Executable.Case
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Constructor from a config (read in from a XML file)
- change(Genotype) - Method in interface VCF.Changers.GenotypeChanger
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Change the given genotype
- change(Genotype) - Method in class VCF.Changers.MaxDepthNoReadsChanger
- change(Genotype) - Method in class VCF.Changers.MinDepthMissingChanger
- change(Position) - Method in interface VCF.Changers.PositionChanger
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Change the given genotype
- change(Position) - Method in class VCF.Changers.RenameFormatChanger
- change(Position) - Method in class VCF.Changers.StandardizeCountsFormatChanger
- change(VCF) - Method in class VCF.Filters.PositionFilter
- change(VCF) - Method in class VCF.Filters.SampleFilter
- change(VCF) - Method in interface VCF.Filters.VCFFilter
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Apply this filter to a VCF
- characteristics() - Method in class Utils.Distribution.ComparableDistributionCollector
- characteristics() - Method in class Utils.Distribution.DistributionCollector
- ClassList<X,Y> - Class in Executable
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Represents a map of constructors so that a new object of the appropriate child class (given by a string) can be constructed.
- ClassList() - Constructor for class Executable.ClassList
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Default constructor
- combine(double[][][], double[][][], int[][][]) - Method in interface Combiner.Combiner
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Combines imputed and inferred genotypes for all genotypes in a table
- combine(double[][][], double[][][], int[][][]) - Method in class Combiner.MaxDepthCombiner
- combine(List<SingleGenotypeProbability>, List<SingleGenotypeProbability>, List<SingleGenotypeReads>) - Method in interface Combiner.Combiner
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Combines imputed and inferred genotypes for a list of genotypes
- combine(List<SingleGenotypeProbability>, List<SingleGenotypeProbability>, List<SingleGenotypeReads>) - Method in class Combiner.MaxDepthCombiner
- combiner() - Method in class Utils.Distribution.ComparableDistributionCollector
- combiner() - Method in class Utils.Distribution.DistributionCollector
- Combiner - package Combiner
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Provides classes for combining called and imputed genotyped probabilities.
- Combiner - Interface in Combiner
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Combines imputed and inferred genotypes to give a final called genotype
- CombinerOption - Class in Executable
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Represents the combiner options to LinkImpute
- CombinerOption(Combiner) - Constructor for class Executable.CombinerOption
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Constructor for when the combiner isn't optimizable.
- CombinerOption(OptimizeCombiner) - Constructor for class Executable.CombinerOption
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Constructor for when the combiner is optimizable
- CombinerOption(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Executable.CombinerOption
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Constructor from a config (read in from a XML file)
- ComparableDistribution<V extends java.lang.Comparable<V>> - Class in Utils.Distribution
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Represents a distribution of comparable discrete objects.
- ComparableDistribution(CountMap<V>) - Constructor for class Utils.Distribution.ComparableDistribution
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Default constructor
- ComparableDistributionCollector<V extends java.lang.Comparable<V>> - Class in Utils.Distribution
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Collector for use with streams that creates a ComparableDistribution from a stream of objects
- ComparableDistributionCollector() - Constructor for class Utils.Distribution.ComparableDistributionCollector
- compare(Integer, Integer) - Method in class Utils.SortByIndexDouble
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Overrides the default compare method and instead compares the ith and jth element of the values array
- constantDistribution(W) - Static method in class Utils.Distribution.ComparableDistribution
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Creates a constant distribution - ia distribution containing a single object
- constantDistribution(W) - Static method in class Utils.Distribution.Distribution
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Creates a constant distribution - ia distribution containing a single object
- copy() - Method in class VCF.Genotype
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Create a copy of the genotype
- correct() - Method in class Accuracy.AccuracyStats
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Return the total number of genotypes that are correct
- CORRECT - Accuracy.AccuracyCalculator.AccuracyMethod
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Use percent correct
- correlation() - Method in class Accuracy.AccuracyStats
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Returns the overall correlation
- correlation(List<SingleGenotypeCall>, List<SingleGenotypeCall>, List<SingleGenotypeMasked>) - Static method in class Accuracy.AccuracyCalculator
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Calculates the correlation between correct and imputed genotypes
- Correlation - Class in Utils.Correlation
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Calculates correlations.
- Correlation() - Constructor for class Utils.Correlation.Correlation
- CORRELATION - Accuracy.AccuracyCalculator.AccuracyMethod
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Use correlation
- countGreaterThan(V) - Method in class Utils.Distribution.ComparableDistribution
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Returns the count of objects greater than the given object
- countGreaterThanEqual(V) - Method in class Utils.Distribution.ComparableDistribution
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Returns the count of objects greater than or equal to the given object
- countLessThan(V) - Method in class Utils.Distribution.ComparableDistribution
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Returns the count of objects less than the given object
- countLessThanEqual(V) - Method in class Utils.Distribution.ComparableDistribution
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Returns the count of objects less than or equal the given object
- CountMap<V> - Class in Utils.Distribution
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Keeps counts of an object
- CountMap() - Constructor for class Utils.Distribution.CountMap
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Default constructor
- critical(String) - Static method in class Utils.Log
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Log a new critical message
- CRITICAL - Utils.Log.Level
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Only outputs critical messages
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