Package picard.analysis.artifacts

Class SequencingArtifactMetrics.BaitBiasDetailMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
Enclosing class:
SequencingArtifactMetrics
@DocumentedFeature(groupName="Metrics", summary="Metrics") public static class SequencingArtifactMetrics.BaitBiasDetailMetrics extends htsjdk.samtools.metrics.MetricBase
Bait bias artifacts broken down by context.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    char
    ALT_BASE
    The (upper-case) alternative base that is called as a result of DNA damage.
    String
    CONTEXT
    The sequence context to which the analysis is constrained.
    double
    ERROR_RATE
    The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).
    long
    FWD_CXT_ALT_BASES
    The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
    long
    FWD_CXT_REF_BASES
    The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
    double
    FWD_ERROR_RATE
    The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).
    String
    LIBRARY
    The name of the library being assayed.
    double
    QSCORE
    The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
    char
    REF_BASE
    The (upper-case) original base on the reference strand.
    long
    REV_CXT_ALT_BASES
    The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
    long
    REV_CXT_REF_BASES
    The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
    double
    REV_ERROR_RATE
    The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).
    String
    SAMPLE_ALIAS
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    BaitBiasDetailMetrics()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    calculateDerivedStatistics()
    Calculate the error rate given the raw counts.
    int
    compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics o)
     

    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

    • 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.

    • FWD_CXT_REF_BASES

      public long FWD_CXT_REF_BASES
      The number of REF_BASE:REF_BASE alignments at sites with the given reference context.

    • FWD_CXT_ALT_BASES

      public long FWD_CXT_ALT_BASES
      The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.

    • REV_CXT_REF_BASES

      public long REV_CXT_REF_BASES
      The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.

    • REV_CXT_ALT_BASES

      public long REV_CXT_ALT_BASES
      The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.

    • FWD_ERROR_RATE

      public double FWD_ERROR_RATE
      The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).

    • REV_ERROR_RATE

      public double REV_ERROR_RATE
      The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).

    • ERROR_RATE

      public double ERROR_RATE
      The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).

    • QSCORE

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

  • Constructor Details

    • BaitBiasDetailMetrics

      public BaitBiasDetailMetrics()

  • Method Details

    • calculateDerivedStatistics

      public void calculateDerivedStatistics()
      Calculate the error rate given the raw counts. Negative rates are set to MIN_ERROR.

    • compareTo

      public int compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics o)