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BiallelicFilter - Class in VCF.Filters
Filters positions for biallelic positions
BiallelicFilter() - Constructor for class VCF.Filters.BiallelicFilter
Constructor
BiallelicFilter(HierarchicalConfiguration<ImmutableNode>) - Constructor for class VCF.Filters.BiallelicFilter
Constructor from a config (read in from a XML file)
BiasedBinomialCaller - Class in Callers
A biased binomial caller, that is one where each read is not equally likely in the case of a hetrozygote
BiasedBinomialCaller(double, double) - Constructor for class Callers.BiasedBinomialCaller
Creates a biased caller with the given error and bias
BiasedBinomialCaller(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Callers.BiasedBinomialCaller
Creates the caller from the given configuration
BinomialCaller - Class in Callers
Simple binomial caller
BinomialCaller(double) - Constructor for class Callers.BinomialCaller
Creates the caller with the given error
BinomialCaller(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Callers.BinomialCaller
Creates the caller from the given configuration
brief(String) - Static method in class Utils.Log
Log a new brief message
BRIEF - Utils.Log.Level
Only output brief messages
BYSAMPLE - Accuracy.DepthMask.Method
First select a sample at random then a maskable genotype from that sample
BYSNP - Accuracy.DepthMask.Method
First select a snp at random then a maskable genotype from that snp
ByteMapper - Interface in VCF.Mappers
Maps from a text string to a byte
ByteToGeno - Class in VCF
A simple convenience class used to convert a byte genotype to a text string representing it
ByteToGeno() - Constructor for class VCF.ByteToGeno
Default constructor
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