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A

accuracy(byte[][], byte[][]) - Method in class Mask.Mask
Calculates imputation accuracy
add(E, V) - Method in class Utils.TopQueue
Attempts to add a new entry
add(String, String) - Method in class Files.VCFData.Data
 
addFormat(FormatDefinition) - Method in class Files.VCFData.Position
 
addFormat(FormatDefinition, Position, String[]) - Method in class Files.VCFData.Data
 
addFormatDefinition(FormatDefinition) - Method in class Files.VCFData.Meta
 
addPosition(Position, String[]) - Method in class Files.VCFData.Data
 
addPosition(String, Set<InfoDefinition>, Set<FormatDefinition>) - Method in class Files.VCFData.Data
 
asArray() - Method in class Files.PlinkNumeric
Get the genotypes as an array.
asArray() - Method in class Files.PlinkPed
Get the genotypes as an array.
asArray(FormatDefinition, Mapper<V>) - Method in class Files.VCFData.Data
 
asArrayTransposed() - Method in class Files.PlinkNumeric
Get the genotypes as an array.
asArrayTransposed() - Method in class Files.PlinkPed
Get the genotypes as an array.
asArrayTransposed(FormatDefinition, Mapper<V>) - Method in class Files.VCFData.Data
 
asByteArray(FormatDefinition, ByteMapper) - Method in class Files.VCFData.Data
 
asByteArrayTransposed(FormatDefinition, ByteMapper) - Method in class Files.VCFData.Data
 
asDoubleArray(FormatDefinition, DoubleMapper) - Method in class Files.VCFData.Data
 
asDoubleArrayTransposed(FormatDefinition, DoubleMapper) - Method in class Files.VCFData.Data
 
asIntArray(FormatDefinition, IntegerMapper) - Method in class Files.VCFData.Data
 
asIntArrayTransposed(FormatDefinition, IntegerMapper) - Method in class Files.VCFData.Data
 
asStringArray(FormatDefinition) - Method in class Files.VCFData.Data
 
asStringArray(FormatDefinition, StringMapper) - Method in class Files.VCFData.Data
 
asStringArrayTransposed(FormatDefinition) - Method in class Files.VCFData.Data
 
asStringArrayTransposed(FormatDefinition, StringMapper) - Method in class Files.VCFData.Data
 
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