Class GenotypeQualityFilter

    • Constructor Detail

      • GenotypeQualityFilter

        public GenotypeQualityFilter​(int gqThreshold,
                                     String sample)
        Constructor for a filter that will keep VC for which the genotype quality (GQ) of sample passes a threshold. If sample is null, the first genotype in the variant context will be used.
        Parameters:
        gqThreshold - the smallest value of GQ that this filter will pass
        sample - the name of the sample in the variant context whose genotype should be examined.
      • GenotypeQualityFilter

        public GenotypeQualityFilter​(int gqThreshold)
        Constructor as above that doesn't take a sample, instead it will look at the first genotype of the variant context.
        Parameters:
        gqThreshold - the smallest value of GQ that this filter will pass
    • Method Detail

      • test

        public boolean test​(VariantContext variantContext)
        Specified by:
        test in interface Predicate<VariantContext>
        Parameters:
        variantContext - the record to examine for GQ
        Returns:
        true if variantContext is to be kept, otherwise false Assumes that this.sample is a sample in the variantContext, if not null, otherwise looks for the first genotype (and assumes it exists).