Class CollectOxoGMetrics.CpcgMetrics

  • Enclosing class:
    CollectOxoGMetrics

    @DocumentedFeature(groupName="Metrics",
                       summary="Metrics")
    public static final class CollectOxoGMetrics.CpcgMetrics
    extends htsjdk.samtools.metrics.MetricBase
    Metrics class for outputs.
    • Field Summary

      Fields 
      Modifier and Type Field Description
      long ALT_NONOXO_BASES
      The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause
      long ALT_OXO_BASES
      The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.
      long C_REF_ALT_BASES
      The number of alt (A/T) basecalls observed at sites where the genome reference == C.
      double C_REF_OXO_ERROR_RATE
      The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs.
      double C_REF_OXO_Q
      C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
      long C_REF_REF_BASES
      The number of ref basecalls observed at sites where the genome reference == C.
      String CONTEXT
      The sequence context being reported on.
      long G_REF_ALT_BASES
      The number of alt (A/T) basecalls observed at sites where the genome reference == G.
      double G_REF_OXO_ERROR_RATE
      The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs.
      double G_REF_OXO_Q
      G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
      long G_REF_REF_BASES
      The number of ref basecalls observed at sites where the genome reference == G.
      String LIBRARY
      The name of the library being assayed.
      double OXIDATION_ERROR_RATE
      The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES
      double OXIDATION_Q
      -10 * log10(OXIDATION_ERROR_RATE)
      long REF_NONOXO_BASES
      The number of reference alleles observed as C in read 1 and G in read 2.
      long REF_OXO_BASES
      The number of reference alleles observed as G in read 1 and C in read 2.
      long REF_TOTAL_BASES
      The total number of reference alleles observed
      String SAMPLE_ALIAS
      The name of the sample being assayed.
      long TOTAL_BASES
      The total number of basecalls observed at all sites.
      int TOTAL_SITES
      The total number of sites that had at least one base covering them.
    • Constructor Summary

      Constructors 
      Constructor Description
      CpcgMetrics()  
    • Field Detail

      • SAMPLE_ALIAS

        public String SAMPLE_ALIAS
        The name of the sample being assayed.
      • LIBRARY

        public String LIBRARY
        The name of the library being assayed.
      • CONTEXT

        public String CONTEXT
        The sequence context being reported on.
      • TOTAL_SITES

        public int TOTAL_SITES
        The total number of sites that had at least one base covering them.
      • TOTAL_BASES

        public long TOTAL_BASES
        The total number of basecalls observed at all sites.
      • REF_NONOXO_BASES

        public long REF_NONOXO_BASES
        The number of reference alleles observed as C in read 1 and G in read 2.
      • REF_OXO_BASES

        public long REF_OXO_BASES
        The number of reference alleles observed as G in read 1 and C in read 2.
      • REF_TOTAL_BASES

        public long REF_TOTAL_BASES
        The total number of reference alleles observed
      • ALT_NONOXO_BASES

        public long ALT_NONOXO_BASES
        The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause
      • ALT_OXO_BASES

        public long ALT_OXO_BASES
        The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.
      • OXIDATION_ERROR_RATE

        public double OXIDATION_ERROR_RATE
        The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES
      • OXIDATION_Q

        public double OXIDATION_Q
        -10 * log10(OXIDATION_ERROR_RATE)
      • C_REF_REF_BASES

        public long C_REF_REF_BASES
        The number of ref basecalls observed at sites where the genome reference == C.
      • G_REF_REF_BASES

        public long G_REF_REF_BASES
        The number of ref basecalls observed at sites where the genome reference == G.
      • C_REF_ALT_BASES

        public long C_REF_ALT_BASES
        The number of alt (A/T) basecalls observed at sites where the genome reference == C.
      • G_REF_ALT_BASES

        public long G_REF_ALT_BASES
        The number of alt (A/T) basecalls observed at sites where the genome reference == G.
      • C_REF_OXO_ERROR_RATE

        public double C_REF_OXO_ERROR_RATE
        The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base.
      • C_REF_OXO_Q

        public double C_REF_OXO_Q
        C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
      • G_REF_OXO_ERROR_RATE

        public double G_REF_OXO_ERROR_RATE
        The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs. a G reference base.
      • G_REF_OXO_Q

        public double G_REF_OXO_Q
        G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
    • Constructor Detail

      • CpcgMetrics

        public CpcgMetrics()