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- test(Position) - Method in class VCF.Filters.BiallelicFilter
- test(Position) - Method in class VCF.Filters.HasDepthFilter
- test(Position) - Method in class VCF.Filters.MAFFilter
- test(Position) - Method in class VCF.Filters.ParalogHWFilter
- test(Position) - Method in class VCF.Filters.PositionFilter
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Tests whether a position should be filtered out
- test(Position) - Method in class VCF.Filters.PositionMissing
- test(Sample) - Method in class VCF.Filters.SampleFilter
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Tests whether a sample should be filtered out
- test(Sample) - Method in class VCF.Filters.SampleMissing
- TEXT - Utils.Progress.ProgressFactory.ProgressType
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The text indicator (TextProgress)
- TEXTBAR - Utils.Progress.ProgressFactory.ProgressType
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The text bar indicator (TextBarProgress)
- TextBarProgress - Class in Utils.Progress
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Draws and updates a progress bar to standard out
- TextBarProgress(long) - Constructor for class Utils.Progress.TextBarProgress
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Constructor
- TextProgress - Class in Utils.Progress
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Shows progress as a simple tex output showing" number complete / total number"
- TextProgress(long) - Constructor for class Utils.Progress.TextProgress
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Constructor
- topn(byte[][], int) - Method in class Utils.Correlation.Correlation
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Returns the position of the most correlated arrays for every array.
- topnvalues(byte[][], int) - Method in class Utils.Correlation.Correlation
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Similar to topn except it returns the correlations rather than the positions
- TopQueue - Class in Utils
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Queue that keeps only the entries with the top values
- TopQueue(int) - Constructor for class Utils.TopQueue
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Constructor
- toString() - Method in class VCF.Genotype
- toString() - Method in class VCF.Position
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Returns the position meta data as a string
- toString() - Method in class VCF.PositionMeta
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Gets a string representing just the chromosome and the position of the position.
- total() - Method in class Accuracy.AccuracyStats
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Return the total number of genotypes used in the accuracy calculation
- toText() - Method in class VCF.Position
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Returns the entire position (including data) as a string
- toText() - Method in class VCF.PositionMeta
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Get a string for all the meta data for the position
- transpose(byte[][]) - Static method in class Utils.Matrix
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Transposes a matrix
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