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A

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