A B C D E F G H I K L M N O P R S T U V W 

D

debug(String) - Static method in class Utils.Log
Log a new debug message
DEBUG - Utils.Log.Level
Output debug level messages
depthAccuracy(int) - Method in class Accuracy.AccuracyStats
Returns the accuracy for a certain depth (number of reads)
depthCorrect(int) - Method in class Accuracy.AccuracyStats
Return the number of genotypes that are correct that have the given depth (read count)
depthCorrelation(int) - Method in class Accuracy.AccuracyStats
Returns the correlation for a certain depth (number of reads)
depthGenoAccuracy(int, byte) - Method in class Accuracy.AccuracyStats
Return the accuracy for a given depth (read count) and true genotype
depthGenoCorrect(int, byte) - Method in class Accuracy.AccuracyStats
Return the number of genotypes that are correct that have the given depth (read count) and true genotype
depthGenoTotal(int, byte) - Method in class Accuracy.AccuracyStats
Return the number of genotypes used in the accuracy calculation that have the give depth (read count) and true genotype
DepthMapper - Class in VCF.Mappers
Maps from a string representing read depths to an integer array of read depths
DepthMapper() - Constructor for class VCF.Mappers.DepthMapper
 
DepthMask - Class in Accuracy
Creates a mask where reads for some genotypes are masked to a given depth
DepthMask(int[][][], int, int, int, DepthMask.Method, Caller) - Constructor for class Accuracy.DepthMask
Masks a given number of genotypes to a given depth
DepthMask(int[][][], int, int, int, Caller) - Constructor for class Accuracy.DepthMask
Masks a given number of genotypes to a given depth
DepthMask(int[][][], int, int, ComparableDistribution<Integer>, DepthMask.Method, List<SingleGenotypePosition>, Caller) - Constructor for class Accuracy.DepthMask
Masks a given number of genotypes to a given distribution of depths
DepthMask(int[][][], int, int, ComparableDistribution<Integer>, Caller) - Constructor for class Accuracy.DepthMask
Masks a given number of genotypes to a given depth
DepthMask.Method - Enum in Accuracy
Represents the method to be used to select genotypes to be masked
DepthMaskFactory - Class in Accuracy
Utility class for easily creating multiple DepthMasks with the same parameters
DepthMaskFactory(int, int, int, DepthMask.Method) - Constructor for class Accuracy.DepthMaskFactory
Default constructor
DepthMaskFactory(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Accuracy.DepthMaskFactory
Creates the factory from the given configuration
depthTotal(int) - Method in class Accuracy.AccuracyStats
Return the number of genotypes used in the accuracy calculation that have the given depth (read count)
Descent - Class in Utils.Optimize
Optimizes the input to a function of type MultipleIntegerValue using the descent method
Descent() - Constructor for class Utils.Optimize.Descent
 
detail(String) - Static method in class Utils.Log
Log a new detail message
DETAIL - Utils.Log.Level
Output detailed messages
Distribution<V> - Class in Utils.Distribution
Represents a discrete distribution of objects.
Distribution(CountMap<V>) - Constructor for class Utils.Distribution.Distribution
Default constructor
DistributionCollector<V> - Class in Utils.Distribution
Collector for use with streams that creates a Distribution from a stream of objects
DistributionCollector() - Constructor for class Utils.Distribution.DistributionCollector
 
done() - Method in class Utils.Progress.DotsProgress
Call when another task has been completed
done() - Method in interface Utils.Progress.Progress
Called to indicate another task is complete
done() - Method in class Utils.Progress.SilentProgress
 
done() - Method in class Utils.Progress.TextBarProgress
Call when another task has been completed
done() - Method in class Utils.Progress.TextProgress
 
done(int) - Method in class Utils.Progress.DotsProgress
Call when more tasks have been completed
done(int) - Method in interface Utils.Progress.Progress
Called to indicate multiple tasks are complete
done(int) - Method in class Utils.Progress.SilentProgress
 
done(int) - Method in class Utils.Progress.TextBarProgress
Call when more tasks have been completed
done(int) - Method in class Utils.Progress.TextProgress
 
DOTS - Utils.Progress.ProgressFactory.ProgressType
The dots indicator (DotsProgress)
DotsProgress - Class in Utils.Progress
Draws and updates a progress bar to standard out
DotsProgress(long) - Constructor for class Utils.Progress.DotsProgress
Constructor
DoubleMapper - Interface in VCF.Mappers
Maps from a text string to a double
A B C D E F G H I K L M N O P R S T U V W 
Skip navigation links