A B C D E F G H I K L M N O P R S T U V W X
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- accumulator() - Method in class Utils.Distribution.ComparableDistributionCollector
- accumulator() - Method in class Utils.Distribution.DistributionCollector
- accuracy() - Method in class Accuracy.AccuracyStats
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Returns the overall accuracy
- accuracy(List<SingleGenotypeCall>, List<SingleGenotypeCall>) - Static method in class Accuracy.AccuracyCalculator
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Calculates the percentage of genotypes called correctly
- Accuracy - package Accuracy
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Provides classes for calculating accuracy.
- AccuracyCalculator - Class in Accuracy
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Calculates accuracy statistics
- AccuracyCalculator.AccuracyMethod - Enum in Accuracy
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Represents the accuracy method to be used for optimization
- accuracyStats(List<SingleGenotypeCall>, List<SingleGenotypeCall>, List<SingleGenotypeMasked>) - Static method in class Accuracy.AccuracyCalculator
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Calculates various statistics concerning the genotypes called correctly
- AccuracyStats - Class in Accuracy
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Represents accuracy statistics
- add(int, double) - Method in class Utils.TopQueue
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Attempts to add a new entry
- add(String, Function<X, Y>) - Method in class Executable.ClassList
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Add a new child class
- add(V) - Method in class Utils.Distribution.CountMap
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Adds a single instance of the give object.
- add(V, Integer) - Method in class Utils.Distribution.CountMap
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Adds multiple instances of the give object.
- addAll(CountMap<V>) - Method in class Utils.Distribution.CountMap
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Add the members of another count map
- addData(String) - Method in class VCF.Genotype
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Add data to the genotype.
- addFormat(String, String) - Method in class VCF.Meta
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Adds a format to the meta information
- AlgorithmException - Exception in Exceptions
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Exception for when there is a problem with one of the algorithms
- AlgorithmException() - Constructor for exception Exceptions.AlgorithmException
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Default constructor
- AlgorithmException(String) - Constructor for exception Exceptions.AlgorithmException
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Constructor that takes a message
- ALL - Accuracy.DepthMask.Method
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Select from all maskable genotypes at random
- allCounts() - Method in class Utils.Distribution.ComparableDistribution
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Get a map from object to count for all objects
- allCounts() - Method in class Utils.Distribution.Distribution
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Gets a stream of (object, count) pairs
- allProportions() - Method in class Utils.Distribution.ComparableDistribution
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Got a map from object to proportion (of total count) for each object
- allProportions() - Method in class Utils.Distribution.Distribution
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Get a stream of (object, proportion) pairs
- applyFilters(VCF) - Method in class Executable.Case
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Apply the filters of this case to a VCF
- asArray(String, Mapper<V>) - Method in class VCF.VCF
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Gets data from the genotypes in the VCF as an array
- asArrayTransposed(String, Mapper<V>) - Method in class VCF.VCF
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Gets data from the genotypes in the VCF as a transposed array
- asByteArray(String, ByteMapper) - Method in class VCF.VCF
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Gets data from the genotypes in the VCF as a byte array
- asByteArrayTransposed(String, ByteMapper) - Method in class VCF.VCF
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Gets data from the genotypes in the VCF as a transposed byte array
- asDoubleArray(String, DoubleMapper) - Method in class VCF.VCF
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Gets data from the genotypes in the VCF as a double array
- asDoubleArrayTransposed(String, DoubleMapper) - Method in class VCF.VCF
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Gets data from the genotypes in the VCF as a transposed double array
- asIntegerArray(String, IntegerMapper) - Method in class VCF.VCF
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Gets data from the genotypes in the VCF as an integer array
- asIntegerArrayTransposed(String, IntegerMapper) - Method in class VCF.VCF
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Gets data from the genotypes in the VCF as a transposed integer array
- Available - Class in Executable
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Class that gets the appropiate object for filters and callers given the configuration describing the filter or caller
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