Class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
Enclosing class:
CollectHiSeqXPfFailMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") 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 Details

    • 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 Details

    • PFFailSummaryMetric

      public PFFailSummaryMetric(String tile)
    • PFFailSummaryMetric

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

    • merge

      Adds the non-calculated fields from the other metric to this one.
      Parameters:
      metric -
    • calculateDerivedFields

      public void calculateDerivedFields()