Class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric

  • Enclosing class:
    CollectHiSeqXPfFailMetrics

    public static class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
    extends htsjdk.samtools.metrics.MetricBase
    Metrics produced by the GetHiSeqXPFFailMetrics program. Used to diagnose lanes from HiSeqX Sequencing, providing the number and fraction of each of the reasons that reads could have not passed PF. Possible reasons are EMPTY (reads from empty wells with no template strand), POLYCLONAL (reads from wells that had more than one strand cloned in them), MISALIGNED (reads from wells that are near the edge of the tile), UNKNOWN (reads that didn't pass PF but couldn't be diagnosed)
    • Field Detail

      • TILE

        public String TILE
        The Tile that is described by this metric. Can be a string (like "All") to mean some marginal over tiles. *
      • READS

        public int READS
        The total number of reads examined
      • PF_FAIL_READS

        public int PF_FAIL_READS
        The number of non-PF reads in this tile.
      • PCT_PF_FAIL_READS

        public double PCT_PF_FAIL_READS
        The fraction of PF_READS
      • PF_FAIL_EMPTY

        public int PF_FAIL_EMPTY
        The number of non-PF reads in this tile that are deemed empty.
      • PCT_PF_FAIL_EMPTY

        public double PCT_PF_FAIL_EMPTY
        The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
      • PF_FAIL_POLYCLONAL

        public int PF_FAIL_POLYCLONAL
        The number of non-PF reads in this tile that are deemed multiclonal.
      • PCT_PF_FAIL_POLYCLONAL

        public double PCT_PF_FAIL_POLYCLONAL
        The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
      • PF_FAIL_MISALIGNED

        public int PF_FAIL_MISALIGNED
        The number of non-PF reads in this tile that are deemed "misaligned".
      • PCT_PF_FAIL_MISALIGNED

        public double PCT_PF_FAIL_MISALIGNED
        The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
      • PF_FAIL_UNKNOWN

        public int PF_FAIL_UNKNOWN
        The number of non-PF reads in this tile that have not been classified.
      • PCT_PF_FAIL_UNKNOWN

        public double PCT_PF_FAIL_UNKNOWN
        The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
    • Constructor Detail

      • PFFailSummaryMetric

        public PFFailSummaryMetric​(String tile)
      • PFFailSummaryMetric

        public PFFailSummaryMetric()
        This ctor is necessary for when reading metrics from file
    • Method Detail

      • calculateDerivedFields

        public void calculateDerivedFields()