Class IndelErrorCalculator

  • All Implemented Interfaces:
    BaseCalculator

    public class IndelErrorCalculator
    extends BaseErrorCalculator
    A calculator that estimates the error rate of the bases it observes for indels only.
    • Field Detail

      • nInsertions

        protected long nInsertions
        Total number of inserts
      • nInsertedBases

        protected long nInsertedBases
        Total number of inserted bases
      • nDeletions

        protected long nDeletions
        Total number of deletions
      • nDeletedBases

        protected long nDeletedBases
        Total number of deleted bases
    • Constructor Detail

      • IndelErrorCalculator

        public IndelErrorCalculator()
    • Method Detail

      • addBase

        public void addBase​(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset,
                            htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef)
        Description copied from class: BaseErrorCalculator
        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 IndelErrorMetric getMetric()
        Returns the metric generated by the observed loci