Package picard.analysis.artifacts

Class ErrorSummaryMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.artifacts.ErrorSummaryMetrics
@DocumentedFeature(groupName="Metrics", summary="Metrics") 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 Details

    • 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 Details

    • ErrorSummaryMetrics

      public ErrorSummaryMetrics()

  • 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