Class OverlappingErrorMetric


  • 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 Detail

      • 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 Detail

      • OverlappingErrorMetric

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

        public OverlappingErrorMetric()
    • Method Detail

      • 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