Class IndelErrorMetric


  • public class IndelErrorMetric
    extends BaseErrorMetric
    Metric to be used for InDel errors
    • Field Detail

      • NUM_INSERTIONS

        public long NUM_INSERTIONS
        The number of insertions. Note: This is not the number of bases that have been inserted.
      • NUM_INSERTED_BASES

        public long NUM_INSERTED_BASES
        The number of inserted bases.
      • INSERTIONS_Q

        public int INSERTIONS_Q
        The (phred) rate of insertions.
      • NUM_DELETIONS

        public long NUM_DELETIONS
        The number of deletions. Note: This is not the number of bases that have been deleted.
      • NUM_DELETED_BASES

        public long NUM_DELETED_BASES
        The number of deleted bases.
      • DELETIONS_Q

        public int DELETIONS_Q
        The (phred) rate of deletions.
    • Constructor Detail

      • IndelErrorMetric

        public IndelErrorMetric​(String covariate,
                                long nTotalBases,
                                long nInserts,
                                long nInsertedBases,
                                long nDeletions,
                                long nDeletedBases)
      • IndelErrorMetric

        public IndelErrorMetric()
    • 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 BaseErrorMetric