Package Callers

Class Caller

    • Constructor Summary

      Constructors 
      Constructor Description
      Caller()  
    • Method Summary

      All Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      double[][][] call​(int[][][] reads)
      Calls genotypes for every genotype
      java.util.List<SingleGenotypeProbability> call​(java.util.List<SingleGenotypeReads> list)
      Call the selected genotypes
      abstract double[] callSingle​(int[] reads)
      Call a single genotype
      abstract org.apache.commons.configuration2.tree.ImmutableNode getConfig()
      Get the config for the caller
      • Methods inherited from class java.lang.Object

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

      • Caller

        public Caller()
    • Method Detail

      • callSingle

        public abstract double[] callSingle​(int[] reads)
        Call a single genotype
        Parameters:
        reads - Array of size two with the reads for the two alleles
        Returns:
        The probability of each genotype (size 3 - genotype 0, 1, 2)
      • call

        public double[][][] call​(int[][][] reads)
        Calls genotypes for every genotype
        Parameters:
        reads - Array of reads, dimensions are number of positions, number of snps, 2 (i.e. counts for each allele)
        Returns:
        The probability of each genotypes
      • call

        public java.util.List<SingleGenotypeProbability> call​(java.util.List<SingleGenotypeReads> list)
        Call the selected genotypes
        Parameters:
        list - The genotypes to call
        Returns:
        The probabilities of each genotype
      • getConfig

        public abstract org.apache.commons.configuration2.tree.ImmutableNode getConfig()
        Get the config for the caller
        Returns:
        The config