Class ErrorSummaryMetrics


  • public class ErrorSummaryMetrics
    extends MergeableMetricBase
    Summary metrics produced by CollectSequencingArtifactMetrics as a roll up of the context-specific error rates, to provide global error rates per type of base substitution. Errors are normalized to the lexically lower reference base and summarized together. E.g. G>T is converted to C>A and merged with data from C>A for reporting.
    • Field Detail

      • REF_BASE

        public char REF_BASE
        The reference base (or it's complement).
      • ALT_BASE

        public char ALT_BASE
        The alternative base (or it's complement).
      • SUBSTITUTION

        public String SUBSTITUTION
        A single string representing the substition from REF_BASE to ALT_BASE for convenience.
      • REF_COUNT

        public long REF_COUNT
        The number of reference bases observed.
      • ALT_COUNT

        public long ALT_COUNT
        The number of alt bases observed.
      • SUBSTITUTION_RATE

        public double SUBSTITUTION_RATE
        The rate of the substitution in question.
    • Constructor Detail

      • ErrorSummaryMetrics

        public ErrorSummaryMetrics()
    • 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