Class SequencingArtifactMetrics.PreAdapterDetailMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
Enclosing class:
SequencingArtifactMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class SequencingArtifactMetrics.PreAdapterDetailMetrics extends htsjdk.samtools.metrics.MetricBase
Pre-adapter artifacts broken down by context.
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    char
    The (upper-case) alternative base that is called as a result of DNA damage.
    long
    The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.
    long
    The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
    The sequence context to which the analysis is constrained.
    double
    The estimated error rate due to this artifact.
    The name of the library being assayed.
    long
    The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.
    long
    The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.
    double
    The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
    char
    The (upper-case) original base on the reference strand.
    The name of the sample being assayed.
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    Calculate the error rate given the raw counts.
    int
     

    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.
    • REF_BASE

      public char REF_BASE
      The (upper-case) original base on the reference strand.
    • ALT_BASE

      public char ALT_BASE
      The (upper-case) alternative base that is called as a result of DNA damage.
    • CONTEXT

      public String CONTEXT
      The sequence context to which the analysis is constrained.
    • PRO_REF_BASES

      public long PRO_REF_BASES
      The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.
    • PRO_ALT_BASES

      public long PRO_ALT_BASES
      The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.
    • CON_REF_BASES

      public long CON_REF_BASES
      The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
    • CON_ALT_BASES

      public long CON_ALT_BASES
      The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.
    • ERROR_RATE

      public double ERROR_RATE
      The estimated error rate due to this artifact. Calculated as max(1e-10, (PRO_ALT_BASES - CON_ALT_BASES) / (PRO_ALT_BASES + PRO_REF_BASES + CON_ALT_BASES + CON_REF_BASES)).
    • QSCORE

      public double QSCORE
      The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
  • Constructor Details

    • PreAdapterDetailMetrics

      public PreAdapterDetailMetrics()
  • Method Details