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