Package picard.sam.SamErrorMetric

Class BaseErrorMetric

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.sam.SamErrorMetric.ErrorMetric
picard.sam.SamErrorMetric.BaseErrorMetric
Direct Known Subclasses:
IndelErrorMetric
@DocumentedFeature(groupName="Metrics", summary="Metrics") public class BaseErrorMetric extends ErrorMetric
An error metric for the errors in bases.

  • Field Details

    • ERROR_BASES

      public long ERROR_BASES
      The number of bases that disagree with the reference

    • Q_SCORE

      public int Q_SCORE
      The (phred) rate of bases that disagree with the reference

  • Constructor Details

    • BaseErrorMetric

      public BaseErrorMetric(String covariate, long totalBases, long errorBases)

    • BaseErrorMetric

      public BaseErrorMetric()

  • 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