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