Package Utils

Class ProbToCallMinDepth


  • public class ProbToCallMinDepth
    extends java.lang.Object
    Converts genotype probabilities to a called genotype
    • Constructor Summary

      Constructors 
      Constructor Description
      ProbToCallMinDepth()
      Default constructor - always calls a genotype, no matter the number of reads
      ProbToCallMinDepth​(int minDepth)
      Creates an instance that will only call a genotype if there are more than the given number of reads for that genotype
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      byte[][] call​(double[][][] probs, int[][][] readCounts)
      Call a table of genotypes
      byte callSingle​(double[] prob, int[] readCounts)
      Call a single genotype
      • Methods inherited from class java.lang.Object

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

      • ProbToCallMinDepth

        public ProbToCallMinDepth()
        Default constructor - always calls a genotype, no matter the number of reads
      • ProbToCallMinDepth

        public ProbToCallMinDepth​(int minDepth)
        Creates an instance that will only call a genotype if there are more than the given number of reads for that genotype
        Parameters:
        minDepth - Minimum number of reads at which to call a genotype
    • Method Detail

      • callSingle

        public byte callSingle​(double[] prob,
                               int[] readCounts)
        Call a single genotype
        Parameters:
        prob - Genotype probabilities
        readCounts - The read counts for that genotype
        Returns:
        The called genotype
      • call

        public byte[][] call​(double[][][] probs,
                             int[][][] readCounts)
        Call a table of genotypes
        Parameters:
        probs - Table of genotype probabilities
        readCounts - Table of read counts
        Returns:
        Table of called genotypes