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