Package picard.analysis

Class CollectQualityYieldMetrics.QualityYieldMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
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