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V

value(double) - Method in interface Utils.Optimize.SingleDoubleValue
Returns the value of a function
value(int[]) - Method in interface Utils.Optimize.MultipleIntegerValue
Returns the value of a function
valueOf(String) - Static method in enum Accuracy.AccuracyCalculator.AccuracyMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Accuracy.DepthMask.Method
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Utils.Log.Level
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum Utils.Progress.ProgressFactory.ProgressType
Returns the enum constant of this type with the specified name.
values() - Static method in enum Accuracy.AccuracyCalculator.AccuracyMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Accuracy.DepthMask.Method
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class Utils.Distribution.CountMap
Get the set of values (that is counts)
values() - Static method in enum Utils.Log.Level
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum Utils.Progress.ProgressFactory.ProgressType
Returns an array containing the constants of this enum type, in the order they are declared.
VCF - package VCF
Provides classes for representing and working with the data in a VCF file.
VCF - Class in VCF
Represents the data from a VCF file
VCF(File) - Constructor for class VCF.VCF
Constructor from a VCF file
VCF(File, List<PositionFilter>) - Constructor for class VCF.VCF
Constructor from a file, filtering positions at read time.
VCF(File, List<PositionFilter>, List<PositionChanger>, List<GenotypeChanger>, List<PositionFilter>, List<String>) - Constructor for class VCF.VCF
Constructor from a file, filtering positions at read time and changing genotypes read in.
VCF(Meta, List<Position>) - Constructor for class VCF.VCF
Create a VCF object from data rather than a file
VCF.Changers - package VCF.Changers
Provides classes for changing a genotype.
VCF.Exceptions - package VCF.Exceptions
Provides classes for VCF Exceptions.
VCF.Filters - package VCF.Filters
Provides classes for filter a VCF.
VCF.Mappers - package VCF.Mappers
Provides classes for mapping the strings in a VCF to other data types.
VCFDataException - Exception in VCF.Exceptions
Exception for when there is a problem with data in the VCF
VCFDataException() - Constructor for exception VCF.Exceptions.VCFDataException
Default constructor
VCFDataException(String) - Constructor for exception VCF.Exceptions.VCFDataException
Constructor that takes a message
VCFDataException(String, Throwable) - Constructor for exception VCF.Exceptions.VCFDataException
Constructor that takes a message and another Throwable as the cause of this exception.
VCFDataLineException - Exception in VCF.Exceptions
Exception for when there is a problem reading in a data line of a VCF
VCFDataLineException() - Constructor for exception VCF.Exceptions.VCFDataLineException
Default constructor
VCFDataLineException(String) - Constructor for exception VCF.Exceptions.VCFDataLineException
Constructor that takes a message
VCFDataLineException(String, Throwable) - Constructor for exception VCF.Exceptions.VCFDataLineException
Constructor that takes a message and another Throwable as the cause of this exception.
VCFException - Exception in VCF.Exceptions
Exception for when there is a problem with the VCF
VCFException() - Constructor for exception VCF.Exceptions.VCFException
Default constructor
VCFException(String) - Constructor for exception VCF.Exceptions.VCFException
Constructor that takes a message
VCFException(String, Throwable) - Constructor for exception VCF.Exceptions.VCFException
Constructor that takes a message and another Throwable as the cause of this exception.
VCFFilter - Interface in VCF.Filters
Represents a VCF filter (either a position filter or a sample filter)
VCFHeaderLineException - Exception in VCF.Exceptions
Exception for when there is a problem reading in a header line of a VCF
VCFHeaderLineException() - Constructor for exception VCF.Exceptions.VCFHeaderLineException
Default constructor
VCFHeaderLineException(String) - Constructor for exception VCF.Exceptions.VCFHeaderLineException
Constructor that takes a message
VCFHeaderLineException(String, Throwable) - Constructor for exception VCF.Exceptions.VCFHeaderLineException
Constructor that takes a message and another Throwable as the cause of this exception.
VCFInputException - Exception in VCF.Exceptions
Exception for when there is a problem reading in a VCF
VCFInputException() - Constructor for exception VCF.Exceptions.VCFInputException
Default constructor
VCFInputException(String) - Constructor for exception VCF.Exceptions.VCFInputException
Constructor that takes a message
VCFInputException(String, Throwable) - Constructor for exception VCF.Exceptions.VCFInputException
Constructor that takes a message and another Throwable as the cause of this exception.
VCFMissingFormatException - Exception in VCF.Exceptions
Exception for when the vcf is missing a required format
VCFMissingFormatException() - Constructor for exception VCF.Exceptions.VCFMissingFormatException
Default constructor
VCFMissingFormatException(String) - Constructor for exception VCF.Exceptions.VCFMissingFormatException
Constructor that takes a message
VCFNoDataException - Exception in VCF.Exceptions
Exception for when there is no data for a given format
VCFNoDataException() - Constructor for exception VCF.Exceptions.VCFNoDataException
Default constructor
VCFNoDataException(String) - Constructor for exception VCF.Exceptions.VCFNoDataException
Constructor that takes a message
VCFUnexpectedDataException - Exception in VCF.Exceptions
Exception for when there is unexpected data for a given format
VCFUnexpectedDataException() - Constructor for exception VCF.Exceptions.VCFUnexpectedDataException
Default constructor
VCFUnexpectedDataException(String) - Constructor for exception VCF.Exceptions.VCFUnexpectedDataException
Constructor that takes a message
VCFUnexpectedDataException(String, Throwable) - Constructor for exception VCF.Exceptions.VCFUnexpectedDataException
Constructor that takes a message and another Throwable as the cause of this exception.
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