Interface PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,​HKEY extends Comparable,​ARGTYPE>

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void acceptRecord​(ARGTYPE args)
      Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
      void addMetricsToFile​(htsjdk.samtools.metrics.MetricsFile<BEAN,​HKEY> file)
      Any metrics collected will be added to the metric file provided.
      void finish()
      When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
    • Method Detail

      • acceptRecord

        void acceptRecord​(ARGTYPE args)
        Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
        Parameters:
        args - Contains SAMRecord, SAMReadGroupRecord, ReferenceSequence of current record and any previously computed values that might be needed for this class
      • finish

        void finish()
        When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
      • addMetricsToFile

        void addMetricsToFile​(htsjdk.samtools.metrics.MetricsFile<BEAN,​HKEY> file)
        Any metrics collected will be added to the metric file provided.
        Parameters:
        file - MetricsFile to which all metrics created by this collector should be added