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I

ImputationOption - Class in Executable
Represents the imputer options to LinkImpute
ImputationOption(Imputer) - Constructor for class Executable.ImputationOption
Constructor for when the imputer isn't optimizable.
ImputationOption(OptimizeImputer) - Constructor for class Executable.ImputationOption
Constructor for when the imputer is optimizable
ImputationOption(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Executable.ImputationOption
Constructor from a config (read in from a XML file)
impute(double[][][], int[][][]) - Method in interface Imputers.Imputer
Imputes a genotype table
impute(double[][][], int[][][]) - Method in class Imputers.KnniLDProb
 
impute(double[][][], int[][][], List<SingleGenotypeProbability>, List<SingleGenotypeMasked>) - Method in interface Imputers.Imputer
Imputes a list of genotypes.
impute(double[][][], int[][][], List<SingleGenotypeProbability>, List<SingleGenotypeMasked>) - Method in class Imputers.KnniLDProb
 
Imputer - Interface in Imputers
Represents an imputer
Imputers - package Imputers
Provides classes for calculating imputed genotype probabilities.
INIException - Exception in Exceptions
Exception for when there is a problem with a ini file
INIException() - Constructor for exception Exceptions.INIException
Default constructor
INIException(String) - Constructor for exception Exceptions.INIException
Constructor that takes a message
INIException(String, Throwable) - Constructor for exception Exceptions.INIException
 
initialise(HierarchicalConfiguration<ImmutableNode>) - Static method in class Utils.Log
Initialise from a configuration
initialise(Log.Level) - Static method in class Utils.Log
Initialise a logger (logs to screen)
initialise(Log.Level, File) - Static method in class Utils.Log
Initialise a logger (logs to file)
Input - Class in Executable
Represents the input to LinkImputeR
Input(File, List<PositionFilter>, File, int, String) - Constructor for class Executable.Input
Constructor
Input(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Executable.Input
Constructor from a config (read in from a XML file)
IntegerMapper - Interface in VCF.Mappers
Maps from a text string to an integer
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