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D
- debug(String) - Static method in class Utils.Log
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Log a new debug message
- DEBUG - Utils.Log.Level
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Output debug level messages
- depthAccuracy(int) - Method in class Accuracy.AccuracyStats
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Returns the accuracy for a certain depth (number of reads)
- depthCorrect(int) - Method in class Accuracy.AccuracyStats
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Return the number of genotypes that are correct that have the given depth (read count)
- depthCorrelation(int) - Method in class Accuracy.AccuracyStats
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Returns the correlation for a certain depth (number of reads)
- depthGenoAccuracy(int, byte) - Method in class Accuracy.AccuracyStats
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Return the accuracy for a given depth (read count) and true genotype
- depthGenoCorrect(int, byte) - Method in class Accuracy.AccuracyStats
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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
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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
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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
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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
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Masks a given number of genotypes to a given depth
- DepthMask(int[][][], int, int, int, Caller) - Constructor for class Accuracy.DepthMask
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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
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Masks a given number of genotypes to a given distribution of depths
- DepthMask(int[][][], int, int, ComparableDistribution<Integer>, Caller) - Constructor for class Accuracy.DepthMask
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Masks a given number of genotypes to a given depth
- DepthMask.Method - Enum in Accuracy
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Represents the method to be used to select genotypes to be masked
- DepthMaskFactory - Class in Accuracy
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Utility class for easily creating multiple DepthMasks with the same parameters
- DepthMaskFactory(int, int, int, DepthMask.Method) - Constructor for class Accuracy.DepthMaskFactory
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Default constructor
- DepthMaskFactory(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Accuracy.DepthMaskFactory
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Creates the factory from the given configuration
- depthTotal(int) - Method in class Accuracy.AccuracyStats
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Return the number of genotypes used in the accuracy calculation that have the given depth (read count)
- Descent - Class in Utils.Optimize
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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
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Log a new detail message
- DETAIL - Utils.Log.Level
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Output detailed messages
- Distribution<V> - Class in Utils.Distribution
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Represents a discrete distribution of objects.
- Distribution(CountMap<V>) - Constructor for class Utils.Distribution.Distribution
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Default constructor
- DistributionCollector<V> - Class in Utils.Distribution
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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
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Call when another task has been completed
- done() - Method in interface Utils.Progress.Progress
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Called to indicate another task is complete
- done() - Method in class Utils.Progress.SilentProgress
- done() - Method in class Utils.Progress.TextBarProgress
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Call when another task has been completed
- done() - Method in class Utils.Progress.TextProgress
- done(int) - Method in class Utils.Progress.DotsProgress
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Call when more tasks have been completed
- done(int) - Method in interface Utils.Progress.Progress
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Called to indicate multiple tasks are complete
- done(int) - Method in class Utils.Progress.SilentProgress
- done(int) - Method in class Utils.Progress.TextBarProgress
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Call when more tasks have been completed
- done(int) - Method in class Utils.Progress.TextProgress
- DOTS - Utils.Progress.ProgressFactory.ProgressType
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The dots indicator (DotsProgress)
- DotsProgress - Class in Utils.Progress
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Draws and updates a progress bar to standard out
- DotsProgress(long) - Constructor for class Utils.Progress.DotsProgress
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Constructor
- DoubleMapper - Interface in VCF.Mappers
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Maps from a text string to a double
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