Package picard.analysis.artifacts

Class SequencingArtifactMetrics.PreAdapterDetailMetrics

  • Enclosing class:
    SequencingArtifactMetrics
    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 ALT_BASE
      The (upper-case) alternative base that is called as a result of DNA damage.
      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.
      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.
      String CONTEXT
      The sequence context to which the analysis is constrained.
      double ERROR_RATE
      The estimated error rate due to this artifact.
      String LIBRARY
      The name of the library being assayed.
      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.
      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.
      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.
      String SAMPLE_ALIAS
      The name of the sample being assayed.

    • 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.

      • 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 Detail

      • PreAdapterDetailMetrics

        public PreAdapterDetailMetrics()