Package picard.sam.SamErrorMetric

Class OverlappingReadsErrorCalculator

java.lang.Object
picard.sam.SamErrorMetric.BaseErrorCalculator
picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
All Implemented Interfaces:
BaseCalculator
public class OverlappingReadsErrorCalculator extends BaseErrorCalculator
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth. This calculator only includes bases that have been read twice in the same template (once from each read) and thus only includes bases that arise from the overlapping part of the reads. Over those bases the Calculator distinguishes between whether the two reads agree with each other but differ from the reference (indicative of a difference between the template and the reference, and when one of the reads agrees with the reference but the other does not which indicates that there might have been a sequencing error in that read.

  • Constructor Details

    • OverlappingReadsErrorCalculator

      public OverlappingReadsErrorCalculator()

  • 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 OverlappingErrorMetric getMetric()
      Returns the metric generated by the observed loci