Package Executable

Class CombinerOption


  • public class CombinerOption
    extends java.lang.Object
    Represents the combiner options to LinkImpute
    • Constructor Detail

      • CombinerOption

        public CombinerOption​(Combiner combiner)
        Constructor for when the combiner isn't optimizable. May be used when we've already created an optimized combiner.
        Parameters:
        combiner - The combiner
      • CombinerOption

        public CombinerOption​(OptimizeCombiner combiner)
        Constructor for when the combiner is optimizable
        Parameters:
        combiner - The combiner
      • CombinerOption

        public CombinerOption​(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

      • getCombiner

        public Combiner getCombiner​(java.util.List<SingleGenotypeProbability> called,
                                    java.util.List<SingleGenotypeProbability> imputed,
                                    java.util.List<SingleGenotypeReads> reads,
                                    java.util.List<SingleGenotypeCall> correct,
                                    java.util.List<SingleGenotypeMasked> masked)
        Gets a combiner. If the combiner option was for one that was not optimized simply returns that. Else optimizes a combiner and returns the optimized version of it.
        Parameters:
        called - The called genotype probabilities
        imputed - The imputed genotype probabilities
        reads - The reads
        correct - The correct genotypes
        masked - A list of masked genotypes
        Returns:
        A combiner
      • getCombiner

        public Combiner getCombiner()
        Returns the combiner if the combiner option was for a non-optimizable combiner, else throws an exception
        Returns:
        The combiner
      • getConfig

        public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
        Get the combiner options config
        Returns:
        The config