Package picard.sam.SamErrorMetric

Class IndelErrorCalculator

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

    Fields
    Modifier and Type
    Field
    Description
    protected long
    nDeletedBases
    Total number of deleted bases
    protected long
    nDeletions
    Total number of deletions
    protected long
    nInsertedBases
    Total number of inserted bases
    protected long
    nInsertions
    Total number of inserts

  • Constructor Summary

    Constructors
    Constructor
    Description
    IndelErrorCalculator()
     

  • 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
    IndelErrorMetric
    getMetric()
    Returns the metric generated by the observed loci
    String
    getSuffix()
    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

    • 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 Details

    • IndelErrorCalculator

      public IndelErrorCalculator()

  • Method Details

    • 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