Package Imputers

Class KnniLDProbOptimizedCalls

  • All Implemented Interfaces:
    OptimizeImputer<KnniLDProb>

    public class KnniLDProbOptimizedCalls
    extends java.lang.Object
    implements OptimizeImputer<KnniLDProb>
    Represents a KnniLDProb imputer that can be optimized to maximise the number of correctly called genotyped
    • Constructor Detail

      • KnniLDProbOptimizedCalls

        public KnniLDProbOptimizedCalls​(int knownDepth,
                                        AccuracyCalculator.AccuracyMethod method)
        Constructor
        Parameters:
        knownDepth - The read depth above which imputation is not performed and the called probabilities are used instead
        method - The accuracy method to be used
      • KnniLDProbOptimizedCalls

        public KnniLDProbOptimizedCalls​(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
        Constructor from a config (read in from a XML file)
        Parameters:
        params - The config
    • Method Detail

      • getOptimized

        public KnniLDProb getOptimized​(double[][][] callprobs,
                                       int[][][] readCounts,
                                       java.util.List<SingleGenotypeProbability> maskedprobs,
                                       java.util.List<SingleGenotypeMasked> list)
        Description copied from interface: OptimizeImputer
        Get an optimized version of the imputer
        Specified by:
        getOptimized in interface OptimizeImputer<KnniLDProb>
        Parameters:
        callprobs - Original called genotype probabilities
        readCounts - Read counts
        maskedprobs - Masked genotype probabilities
        list - List of masked sites and their genotype
        Returns:
        An optimized imputer
      • getConfig

        public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
        Description copied from interface: OptimizeImputer
        Get the config for this case
        Specified by:
        getConfig in interface OptimizeImputer<KnniLDProb>
        Returns:
        The config