Class ErrorMetric

    • Field Detail

      • PRIOR_ERROR

        protected static double PRIOR_ERROR
      • COVARIATE

        public String COVARIATE
        The value of the covariate define the bases included in this metric
      • TOTAL_BASES

        public long TOTAL_BASES
        The total number of bases included in the calculation of this metric
    • Constructor Detail

      • ErrorMetric

        public ErrorMetric​(String covariate,
                           long totalBases)
      • ErrorMetric

        public ErrorMetric()
    • Method Detail

      • setPriorError

        public static void setPriorError​(double priorError)
      • computeQScore

        protected int computeQScore​(long numberOfErrors)
        compute a qscore given the number of errors and the total number of bases. Uses a false count of 1 int the numerator and 1/PRIOR_ERROR in the denominator.
      • computeQScore

        protected int computeQScore​(long numberOfErrors,
                                    long nTotalBases)
        compute a qscore given the number of errors and the total number of bases. Uses a false count of 1 int the denominator and 1 in the numerator.