Package Imputers

Interface Imputer

  • All Known Implementing Classes:
    KnniLDProb

    public interface Imputer
    Represents an imputer
    • Method Detail

      • impute

        double[][][] impute​(double[][][] probs,
                            int[][][] readCounts)
        Imputes a genotype table
        Parameters:
        probs - Genotype probabilities (from a caller)
        readCounts - Read counts for each genotype
        Returns:
        Table of imputed genotype probabilities
      • impute

        java.util.List<SingleGenotypeProbability> impute​(double[][][] probs,
                                                         int[][][] readCounts,
                                                         java.util.List<SingleGenotypeProbability> maskedprobs,
                                                         java.util.List<SingleGenotypeMasked> list)
        Imputes a list of genotypes. Used to calculate accuracy. Need both unmasked probs (probs) and masked probs (maskedprobs) so that the calculation for each genotype is independent (i.e. using the full reads for the other masked genotypes if they're used in the imputation calculation).
        Parameters:
        probs - Genotype probabilities (from a caller)
        readCounts - Read counts for each genotype
        maskedprobs - Genotype probabilities (from a caller) using masked reads
        list - List of genotypes to impute
        Returns:
        List of imputed genotype probabilities
      • getConfig

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