Interface BaseCalculator

All Known Implementing Classes:
BaseErrorCalculator, IndelErrorCalculator, OverlappingReadsErrorCalculator, SimpleErrorCalculator

public interface BaseCalculator
An interface that can take a collection of bases (provided as SamLocusIterator.RecordAndOffset and SamLocusAndReferenceIterator.SAMLocusAndReference) and generates a ErrorMetric from them.

The Calculator has a suffix which will be used to generate the metric file suffixes.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
    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
  • Method Details

    • getSuffix

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

      ErrorMetric getMetric()
      Returns the metric generated by the observed loci
    • addBase

      void addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
      The function by which new loci are "shown" to the calculator