Class OverlappingErrorMetric

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.sam.SamErrorMetric.ErrorMetric
picard.sam.SamErrorMetric.OverlappingErrorMetric

@DocumentedFeature(groupName="Metrics", summary="Metrics") public class OverlappingErrorMetric extends ErrorMetric
An error metric for the errors invovling bases in the overlapping region of a read-pair. The resulting metric includes error rate information which can be assigned to the reading of the molecular insert DISAGREES_WITH_REF_AND_MATE_ONLY_Q, error rate which can be assigned to events that occured to to the molecular insert before it was loaded onto the flowcell/sequencer DISAGREES_WITH_REFERENCE_ONLY_Q, and an error rate which cannot be explained nicely THREE_WAYS_DISAGREEMENT_ONLY_Q.
  • Field Details

    • NUM_BASES_WITH_OVERLAPPING_READS

      public long NUM_BASES_WITH_OVERLAPPING_READS
      The number of bases for which an overlapping base from the mate read was found
    • NUM_DISAGREES_WITH_REFERENCE_ONLY

      public long NUM_DISAGREES_WITH_REFERENCE_ONLY
      The number of bases that disagree with the reference, but agree with their mate
    • DISAGREES_WITH_REFERENCE_ONLY_Q

      public int DISAGREES_WITH_REFERENCE_ONLY_Q
      The (phred) rate of bases that disagree with the reference, but agree with their mate
    • NUM_DISAGREES_WITH_REF_AND_MATE

      public long NUM_DISAGREES_WITH_REF_AND_MATE
      The number of bases that disagree with both the reference and their mate (which agree with each other)
    • DISAGREES_WITH_REF_AND_MATE_ONLY_Q

      public int DISAGREES_WITH_REF_AND_MATE_ONLY_Q
      The (phred) rate of bases that disagree with both the reference and their mate (which agree with each other)
    • NUM_THREE_WAYS_DISAGREEMENT

      public long NUM_THREE_WAYS_DISAGREEMENT
      The number of bases that disagree with both the reference and their mate (which also disagree)
    • THREE_WAYS_DISAGREEMENT_ONLY_Q

      public int THREE_WAYS_DISAGREEMENT_ONLY_Q
      The (phred) rate of bases that disagree with both the reference and their mate (which also disagree)
  • Constructor Details

    • OverlappingErrorMetric

      public OverlappingErrorMetric(String covariate, long nTotalBases, long nTotalBasesWithOverlappingReads, long nDisagreeWithRefAndMate, long nDisagreeWithReferenceOnly, long nThreeWaysDisagreement)
    • OverlappingErrorMetric

      public OverlappingErrorMetric()
  • Method Details

    • calculateDerivedFields

      public void calculateDerivedFields()
      Description copied from class: MergeableMetricBase
      Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
      Overrides:
      calculateDerivedFields in class MergeableMetricBase