Class ErrorMetric

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.sam.SamErrorMetric.ErrorMetric
Direct Known Subclasses:
BaseErrorMetric, OverlappingErrorMetric

@DocumentedFeature(groupName="Metrics", summary="Metrics") public class ErrorMetric extends MergeableMetricBase
Created by farjoun on 6/26/18.
  • Field Details

    • PRIOR_ERROR

      protected static double PRIOR_ERROR
    • COVARIATE

      public String COVARIATE
      The value of the covariate define the bases included in this metric
    • TOTAL_BASES

      public long TOTAL_BASES
      The total number of bases included in the calculation of this metric
  • Constructor Details

    • ErrorMetric

      public ErrorMetric(String covariate, long totalBases)
    • ErrorMetric

      public ErrorMetric()
  • Method Details

    • setPriorError

      public static void setPriorError(double priorError)
    • computeQScore

      protected int computeQScore(long numberOfErrors)
      compute a qscore given the number of errors and the total number of bases. Uses a false count of 1 int the numerator and 1/PRIOR_ERROR in the denominator.
    • computeQScore

      protected int computeQScore(long numberOfErrors, long nTotalBases)
      compute a qscore given the number of errors and the total number of bases. Uses a false count of 1 int the denominator and 1 in the numerator.