Class CollectQualityYieldMetrics.QualityYieldMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
Direct Known Subclasses:
CollectQualityYieldMetrics.QualityYieldMetricsFlow
Enclosing class:
CollectQualityYieldMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class CollectQualityYieldMetrics.QualityYieldMetrics 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
    • READ_LENGTH

      public int READ_LENGTH
      The average read length of all the reads
    • TOTAL_BASES

      public long TOTAL_BASES
      The total number of bases in all reads
    • PF_BASES

      public long PF_BASES
      The total number of bases in all PF reads
    • Q20_BASES

      public long Q20_BASES
      The number of bases in all reads that achieve quality score 20 or higher
    • PF_Q20_BASES

      public long PF_Q20_BASES
      The number of bases in PF reads that achieve quality score 20 or higher
    • Q30_BASES

      public long Q30_BASES
      The number of bases in all reads that achieve quality score 30 or higher
    • PF_Q30_BASES

      public long PF_Q30_BASES
      The number of bases in PF reads that achieve quality score 30 or higher
    • Q20_EQUIVALENT_YIELD

      public long Q20_EQUIVALENT_YIELD
      The sum of quality scores of all bases divided by 20
    • PF_Q20_EQUIVALENT_YIELD

      public long PF_Q20_EQUIVALENT_YIELD
      The sum of quality scores of all bases in PF reads divided by 20
    • useOriginalQualities

      protected final boolean useOriginalQualities
  • Constructor Details

    • QualityYieldMetrics

      public QualityYieldMetrics()
    • QualityYieldMetrics

      public QualityYieldMetrics(boolean useOriginalQualities)
  • Method Details