Class CollectQualityYieldMetrics.QualityYieldMetrics

    • Field Detail

      • 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 Detail

      • QualityYieldMetrics

        public QualityYieldMetrics()
      • QualityYieldMetrics

        public QualityYieldMetrics​(boolean useOriginalQualities)