A B C D E F G H I K L M N O P R S T U V W 

C

calculate(byte[][]) - Method in class Utils.Correlation.Correlation
Calculates correlations between all pairs of arrays
calculate(byte[], byte[]) - Method in class Utils.Correlation.Correlation
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
Call a table of genotypes
call(double[][][], int[][][]) - Method in class Utils.ProbToCallMinDepth
Call a table of genotypes
call(int[][][]) - Method in class Callers.Caller
Calls genotypes for every genotype
call(List<SingleGenotypeProbability>) - Method in class Utils.ProbToCall
Call a list of genotypes
call(List<SingleGenotypeReads>) - Method in class Callers.Caller
Call the selected genotypes
Caller - Class in Callers
Represents a genotype caller
Caller() - Constructor for class Callers.Caller
 
Callers - package Callers
Provides classes for calculating called genotype probabilities.
callSingle(double[]) - Method in class Utils.ProbToCall
Call a single genotype
callSingle(double[], int[]) - Method in class Utils.ProbToCallMinDepth
Call a single genotype
callSingle(int[]) - Method in class Callers.BiasedBinomialCaller
Calls a genotype based on reads
callSingle(int[], int, int) - Method in class Callers.BiasedBinomialCaller
 
callSingle(int[], int, int) - Method in class Callers.Caller
Call a single genotype
Case - Class in Executable
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
Constructor
Case(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Executable.Case
Constructor from a config (read in from a XML file)
change(Genotype) - Method in interface VCF.Changers.GenotypeChanger
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
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
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
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
Default constructor
combine(double[][][], double[][][], int[][][]) - Method in interface Combiner.Combiner
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
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
Provides classes for combining called and imputed genotyped probabilities.
Combiner - Interface in Combiner
Combines imputed and inferred genotypes to give a final called genotype
CombinerOption - Class in Executable
Represents the combiner options to LinkImpute
CombinerOption(Combiner) - Constructor for class Executable.CombinerOption
Constructor for when the combiner isn't optimizable.
CombinerOption(OptimizeCombiner) - Constructor for class Executable.CombinerOption
Constructor for when the combiner is optimizable
CombinerOption(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Executable.CombinerOption
Constructor from a config (read in from a XML file)
ComparableDistribution<V extends java.lang.Comparable<V>> - Class in Utils.Distribution
Represents a distribution of comparable discrete objects.
ComparableDistribution(CountMap<V>) - Constructor for class Utils.Distribution.ComparableDistribution
Default constructor
ComparableDistributionCollector<V extends java.lang.Comparable<V>> - Class in Utils.Distribution
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
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
Creates a constant distribution - ia distribution containing a single object
constantDistribution(W) - Static method in class Utils.Distribution.Distribution
Creates a constant distribution - ia distribution containing a single object
copy() - Method in class VCF.Genotype
Create a copy of the genotype
correct() - Method in class Accuracy.AccuracyStats
Return the total number of genotypes that are correct
CORRECT - Accuracy.AccuracyCalculator.AccuracyMethod
Use percent correct
correlation() - Method in class Accuracy.AccuracyStats
Returns the overall correlation
correlation(List<SingleGenotypeCall>, List<SingleGenotypeCall>, List<SingleGenotypeMasked>) - Static method in class Accuracy.AccuracyCalculator
Calculates the correlation between correct and imputed genotypes
Correlation - Class in Utils.Correlation
Calculates correlations.
Correlation() - Constructor for class Utils.Correlation.Correlation
 
CORRELATION - Accuracy.AccuracyCalculator.AccuracyMethod
Use correlation
countGreaterThan(V) - Method in class Utils.Distribution.ComparableDistribution
Returns the count of objects greater than the given object
countGreaterThanEqual(V) - Method in class Utils.Distribution.ComparableDistribution
Returns the count of objects greater than or equal to the given object
countLessThan(V) - Method in class Utils.Distribution.ComparableDistribution
Returns the count of objects less than the given object
countLessThanEqual(V) - Method in class Utils.Distribution.ComparableDistribution
Returns the count of objects less than or equal the given object
CountMap<V> - Class in Utils.Distribution
Keeps counts of an object
CountMap() - Constructor for class Utils.Distribution.CountMap
Default constructor
critical(String) - Static method in class Utils.Log
Log a new critical message
CRITICAL - Utils.Log.Level
Only outputs critical messages
A B C D E F G H I K L M N O P R S T U V W 
Skip navigation links