Class SimpleErrorCalculator

  • All Implemented Interfaces:
    BaseCalculator

    public class SimpleErrorCalculator
    extends BaseErrorCalculator
    A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
    • Field Detail

      • nMismatchingBases

        protected long nMismatchingBases
    • Constructor Detail

      • SimpleErrorCalculator

        public SimpleErrorCalculator()
    • Method Detail

      • addBase

        public void addBase​(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset,
                            htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef)
        The function by which new loci are "shown" to the calculator
        Specified by:
        addBase in interface BaseCalculator
        Overrides:
        addBase in class BaseErrorCalculator
      • getSuffix

        public String getSuffix()
        The suffix that pertains to the implementation of aggregation
      • getMetric

        public BaseErrorMetric getMetric()
        Returns the metric generated by the observed loci