Package Combiner

Class MaxDepthCombiner

  • All Implemented Interfaces:
    Combiner

    public class MaxDepthCombiner
    extends java.lang.Object
    implements Combiner
    Combines called and imputed genotype probabilities, only using called genotypes above a given read depth
    • Constructor Summary

      Constructors 
      Constructor Description
      MaxDepthCombiner​(double w, int maxDepth)
      Constructor
      MaxDepthCombiner​(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
      Creates the combiner from the given configuration
    • Constructor Detail

      • MaxDepthCombiner

        public MaxDepthCombiner​(double w,
                                int maxDepth)
        Constructor
        Parameters:
        w - The weight to give to the imputed probabilities
        maxDepth - The depth above which only called genotypes are used
      • MaxDepthCombiner

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

      • combine

        public double[][][] combine​(double[][][] called,
                                    double[][][] imputed,
                                    int[][][] reads)
        Description copied from interface: Combiner
        Combines imputed and inferred genotypes for all genotypes in a table
        Specified by:
        combine in interface Combiner
        Parameters:
        called - The called genotype probabilities
        imputed - The imputed genotype probabilities
        reads - The read counts for each genotype
        Returns:
        The called probabilities
      • getConfig

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