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M

MAFFilter - Class in VCF.Filters
Filters positions based on minor allele frequency
MAFFilter(double, int, int, double) - Constructor for class VCF.Filters.MAFFilter
Constructor
MAFFilter(HierarchicalConfiguration<ImmutableNode>) - Constructor for class VCF.Filters.MAFFilter
Constructor from a config (read in from a XML file)
main(String[]) - Static method in class Executable.LinkImputeR
Main function
map(Byte) - Method in class VCF.ByteToGeno
Maps form byte to string
map(String) - Method in interface VCF.Mappers.ByteMapper
Map from string to byte
map(String) - Method in class VCF.Mappers.DepthMapper
Maps from string representing read depths to an integer array of read depths
map(String) - Method in interface VCF.Mappers.DoubleMapper
Map from string to double
map(String) - Method in class VCF.Mappers.GenoToByte
Maps from string representing a genotype to a byte representation
map(String) - Method in interface VCF.Mappers.IntegerMapper
Map from string to integer
map(String) - Method in interface VCF.Mappers.Mapper
Map from string to object
Mapper<M> - Interface in VCF.Mappers
Maps from string to object
maskedArray() - Method in class Accuracy.DepthMask
Get an array of masked reads.
maskedList() - Method in class Accuracy.DepthMask
Get a list of masked reads
maskedPositions() - Method in class Accuracy.DepthMask
Get a list of masked positions
Matrix - Class in Utils
Matrix utility functions
max() - Method in class Utils.Distribution.ComparableDistribution
Gets the maximum object
MaxDepthCombiner - Class in Combiner
Combines called and imputed genotype probabilities, only using called genotypes above a given read depth
MaxDepthCombiner(double, int) - Constructor for class Combiner.MaxDepthCombiner
Constructor
MaxDepthCombiner(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Combiner.MaxDepthCombiner
Creates the combiner from the given configuration
MaxDepthCombinerOptimizedCalls - Class in Combiner
Gets an optimized MaxDepthCombiner.
MaxDepthCombinerOptimizedCalls(int, AccuracyCalculator.AccuracyMethod) - Constructor for class Combiner.MaxDepthCombinerOptimizedCalls
Constructor
MaxDepthCombinerOptimizedCalls(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Combiner.MaxDepthCombinerOptimizedCalls
Creates the optimizer from the given configuration
MaxDepthNoReadsChanger - Class in VCF.Changers
Changes the genotype (the GT field) of genotype to unknown (./.) if the total number of reads is less than a threshold
MaxDepthNoReadsChanger(int) - Constructor for class VCF.Changers.MaxDepthNoReadsChanger
Constructor
meta() - Method in class VCF.Position
Get the meta data for this position
Meta - Class in VCF
Represents the meta information in a VCF
Meta(List<String>) - Constructor for class VCF.Meta
Constructor from the meta lines in a VCF
min() - Method in class Utils.Distribution.ComparableDistribution
Gets the minimum object
MinDepthMissingChanger - Class in VCF.Changers
Changes the genotype (the GT field) of genotype to unknown (./.) if the total number of reads is less than a threshold
MinDepthMissingChanger(int) - Constructor for class VCF.Changers.MinDepthMissingChanger
Constructor
MultipleIntegerValue - Interface in Utils.Optimize
Represents a function that can be optimized.
MultipleTest - Class in Utils.Optimize
Optimizes the input to a function of type SingleDoubleValue by testing multiple possible input values
MultipleTest(double) - Constructor for class Utils.Optimize.MultipleTest
Constructor
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