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limitedtopn(byte[][], int, Set<Integer>) - Method in class Utils.Correlation.Correlation
Similar to topn except it only considers the given arrays
limitedtopnvalues(byte[][], int, Set<Integer>) - Method in class Utils.Correlation.Correlation
Similar to limitedtopn except it returns correlations
limitTo(V, V) - Method in class Utils.Distribution.ComparableDistribution
Create a new distribution only containing objects between lower and upper
limitToPositions(List<PositionMeta>) - Method in class VCF.VCF
Limits the VCF to the given position.
limitToSamples(List<String>) - Method in class VCF.VCF
Limits the VCF to the given samples.
LinkImputeR - Class in Executable
Main class
log(Log.Level, String) - Static method in class Utils.Log
Log a new message
Log - Class in Utils
Very simple logger.
Log.Level - Enum in Utils
Represents different levels of message output.
LogBiasedBinomialCaller - Class in Callers
A biased binomial caller, that is one where each read is not equally likely in the case of a hetrozygote
LogBiasedBinomialCaller(double, double) - Constructor for class Callers.LogBiasedBinomialCaller
Creates a biased caller with the given error and bias
LogBiasedBinomialCaller(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Callers.LogBiasedBinomialCaller
Creates the caller from the given configuration
LogBinomialCaller - Class in Callers
Simple binomial caller
LogBinomialCaller(double) - Constructor for class Callers.LogBinomialCaller
Creates the caller with the given error
LogBinomialCaller(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Callers.LogBinomialCaller
Creates the caller from the given configuration
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