Package picard.sam.SamErrorMetric

Class IndelErrorMetric

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.sam.SamErrorMetric.ErrorMetric
picard.sam.SamErrorMetric.BaseErrorMetric
picard.sam.SamErrorMetric.IndelErrorMetric
@DocumentedFeature(groupName="Metrics", summary="Metrics") public class IndelErrorMetric extends BaseErrorMetric
Metric to be used for InDel errors

  • Field Details

    • 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 Details

    • IndelErrorMetric

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

    • IndelErrorMetric

      public IndelErrorMetric()

  • 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 BaseErrorMetric