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ParalogHWFilter - Class in VCF.Filters
Filters a position based on a Hardy-Weinburg test.
ParalogHWFilter(double, double) - Constructor for class VCF.Filters.ParalogHWFilter
Constructor
ParalogHWFilter(HierarchicalConfiguration<ImmutableNode>) - Constructor for class VCF.Filters.ParalogHWFilter
Constructor from a config (read in from a XML file)
Pearson - Class in Utils.Correlation
Calculates LD as a simple Pearson correlation
Pearson() - Constructor for class Utils.Correlation.Pearson
 
Position - Class in VCF
Represents a position in a VCF file
Position(PositionMeta, LinkedHashMap<String, String>) - Constructor for class VCF.Position
Constructor
PositionChanger - Interface in VCF.Changers
Changes a position
PositionFilter - Class in VCF.Filters
Represents a position filter
PositionFilter() - Constructor for class VCF.Filters.PositionFilter
 
PositionMeta - Class in VCF
Represents the meta data for a position
PositionMeta(String) - Constructor for class VCF.PositionMeta
Constructor from a string representing the meta data (tab delimited)
PositionMeta(String[]) - Constructor for class VCF.PositionMeta
Constructor from an array of strings representing the meta data
PositionMissing - Class in VCF.Filters
Filters a position based on a maximum allowed amount of missing genotypes
PositionMissing(double, int) - Constructor for class VCF.Filters.PositionMissing
Constructor
PositionMissing(HierarchicalConfiguration<ImmutableNode>) - Constructor for class VCF.Filters.PositionMissing
Constructor from a config (read in from a XML file)
positions() - Method in class VCF.Sample
Gets an array of positions in the sample
positionStream() - Method in class VCF.VCF
Returns a stream of positions in the VCF
PrintStats - Class in Executable
Class used to print stats
PrintStats(File, File, File, File, File, boolean) - Constructor for class Executable.PrintStats
Constructor
PrintStats(String, boolean) - Constructor for class Executable.PrintStats
Constructor that creates file names for the different output based on a root string
PrintStats(HierarchicalConfiguration<ImmutableNode>) - Constructor for class Executable.PrintStats
Constructor from a config (read in from a XML file)
ProbToCall - Class in Utils
Converts genotype probabilities to a called genotype
ProbToCall() - Constructor for class Utils.ProbToCall
Default constructor - always calls a genotype, no matter the probability of the most probable genotype
ProbToCall(double) - Constructor for class Utils.ProbToCall
Creates an instance that will only call a genotype if the most probable genotype has a probability greater than the minProb
ProbToCallMinDepth - Class in Utils
Converts genotype probabilities to a called genotype
ProbToCallMinDepth() - Constructor for class Utils.ProbToCallMinDepth
Default constructor - always calls a genotype, no matter the number of reads
ProbToCallMinDepth(int) - Constructor for class Utils.ProbToCallMinDepth
Creates an instance that will only call a genotype if there are more than the given number of reads for that genotype
ProgrammerException - Exception in Exceptions
Represents an exception an end user should never see
ProgrammerException() - Constructor for exception Exceptions.ProgrammerException
Default constructor
ProgrammerException(Throwable) - Constructor for exception Exceptions.ProgrammerException
Constructor that takes another Throwable as the cause of this exception
Progress - Interface in Utils.Progress
A means for indicating progress to the user
ProgressFactory - Class in Utils.Progress
Factory for creating a progress indicator
ProgressFactory.ProgressType - Enum in Utils.Progress
Represents the types of progress indicators
proportionGreaterThan(V) - Method in class Utils.Distribution.ComparableDistribution
Returns the proportion of objects greater than the given object
proportionGreaterThanEqual(V) - Method in class Utils.Distribution.ComparableDistribution
Returns the proportion of objects greater than or equal to the given object
proportionLessThan(V) - Method in class Utils.Distribution.ComparableDistribution
Returns the proportion of objects less than the given object
proportionLessThanEqual(V) - Method in class Utils.Distribution.ComparableDistribution
Returns the proportion of objects less than or equal to the given object
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