Class CollectOxoGMetrics.CpcgMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.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
    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
    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
    The number of alt (A/T) basecalls observed at sites where the genome reference == C.
    double
    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_ERROR_RATE expressed as a phred-scaled quality score.
    long
    The number of ref basecalls observed at sites where the genome reference == C.
    The sequence context being reported on.
    long
    The number of alt (A/T) basecalls observed at sites where the genome reference == G.
    double
    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_ERROR_RATE expressed as a phred-scaled quality score.
    long
    The number of ref basecalls observed at sites where the genome reference == G.
    The name of the library being assayed.
    double
    The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES
    double
    -10 * log10(OXIDATION_ERROR_RATE)
    long
    The number of reference alleles observed as C in read 1 and G in read 2.
    long
    The number of reference alleles observed as G in read 1 and C in read 2.
    long
    The total number of reference alleles observed
    The name of the sample being assayed.
    long
    The total number of basecalls observed at all sites.
    int
    The total number of sites that had at least one base covering them.
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Methods inherited from class htsjdk.samtools.metrics.MetricBase

    equals, hashCode, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
  • Field Details

    • 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 Details

    • CpcgMetrics

      public CpcgMetrics()