Class SimpleErrorCalculator

java.lang.Object
picard.sam.SamErrorMetric.BaseErrorCalculator
picard.sam.SamErrorMetric.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 Details

    • nMismatchingBases

      protected long nMismatchingBases

  • Constructor Details

    • SimpleErrorCalculator

      public SimpleErrorCalculator()

  • Method Details

    • 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