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 Summary

    Fields
    Modifier and Type
    Field
    Description
    protected long
     
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    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
    Returns the metric generated by the observed loci
    The suffix that pertains to the implementation of aggregation

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • 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