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