Class CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow
Enclosing class:
CollectQualityYieldMetricsFlow

@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow extends MergeableMetricBase
A set of metrics used to describe the general quality of a BAM file
  • Field Details

    • TOTAL_READS

      public long TOTAL_READS
      The total number of reads in the input file
    • PF_READS

      public long PF_READS
      The number of reads that are PF - pass filter
    • MEAN_PF_READ_NUMBER_OF_FLOWS

      public int MEAN_PF_READ_NUMBER_OF_FLOWS
      The average number of flows in PF reads
    • PF_FLOWS

      public long PF_FLOWS
      The total number of flows in all PF reads
    • PF_Q20_FLOWS

      public long PF_Q20_FLOWS
      The number of flows in PF reads that achieve quality score 20 or higher
    • PCT_PF_Q20_FLOWS

      public double PCT_PF_Q20_FLOWS
      The percentage of flows in all reads that achieve quality score 20 or higher
    • PF_Q30_FLOWS

      public long PF_Q30_FLOWS
      The number of flows in PF reads that achieve quality score 30 or higher
    • PCT_PF_Q30_FLOWS

      public double PCT_PF_Q30_FLOWS
      The percentage of flows in all reads that achieve quality score 30 or higher
    • PF_Q20_EQUIVALENT_YIELD

      public long PF_Q20_EQUIVALENT_YIELD
      The sum of quality scores of all flows in PF reads divided by 20
  • Constructor Details

    • QualityYieldMetricsFlow

      public QualityYieldMetricsFlow()
  • Method Details