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T

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