Package Callers

Class BiasedBinomialCaller

  • Direct Known Subclasses:
    BinomialCaller

    public class BiasedBinomialCaller
    extends Caller
    A biased binomial caller, that is one where each read is not equally likely in the case of a hetrozygote
    • Constructor Summary

      Constructors 
      Constructor Description
      BiasedBinomialCaller​(double error, double bias)
      Creates a biased caller with the given error and bias
      BiasedBinomialCaller​(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
      Creates the caller from the given configuration
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double[] callSingle​(int[] d)
      Calls a genotype based on reads
      org.apache.commons.configuration2.tree.ImmutableNode getConfig()
      Get the config for the caller
      double getError()
      Get the eror rate used in the caller
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • BiasedBinomialCaller

        public BiasedBinomialCaller​(double error,
                                    double bias)
        Creates a biased caller with the given error and bias
        Parameters:
        error - The error rate
        bias - The bias - given as the probability of the allele coded 0
      • BiasedBinomialCaller

        public BiasedBinomialCaller​(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
        Creates the caller from the given configuration
        Parameters:
        params - The configuration
    • Method Detail

      • callSingle

        public double[] callSingle​(int[] d)
        Calls a genotype based on reads
        Specified by:
        callSingle in class Caller
        Parameters:
        d - The reads
        Returns:
        The called genotype
      • getConfig

        public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
        Description copied from class: Caller
        Get the config for the caller
        Specified by:
        getConfig in class Caller
        Returns:
        The config
      • getError

        public double getError()
        Get the eror rate used in the caller
        Returns:
        The error rate