Package picard.illumina

Class IlluminaBasecallingMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.illumina.IlluminaBasecallingMetrics
@DocumentedFeature(groupName="Metrics", summary="Metrics") public class IlluminaBasecallingMetrics extends htsjdk.samtools.metrics.MetricBase
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis. Averages and means are taken over all tiles.

  • Field Details

    • LANE

      public String LANE
      The lane for which the metrics were calculated.

    • MOLECULAR_BARCODE_SEQUENCE_1

      public String MOLECULAR_BARCODE_SEQUENCE_1
      The barcode sequence for which the metrics were calculated.

    • MOLECULAR_BARCODE_NAME

      public String MOLECULAR_BARCODE_NAME
      The barcode name for which the metrics were calculated.

    • TOTAL_BASES

      public long TOTAL_BASES
      The total number of bases assigned to the index.

    • PF_BASES

      public long PF_BASES
      The total number of passing-filter bases assigned to the index.

    • TOTAL_READS

      public long TOTAL_READS
      The total number of reads assigned to the index.

    • PF_READS

      public long PF_READS
      The total number of passing-filter reads assigned to the index.

    • TOTAL_CLUSTERS

      public long TOTAL_CLUSTERS
      The total number of clusters assigned to the index.

    • PF_CLUSTERS

      public long PF_CLUSTERS
      The total number of PF clusters assigned to the index.

    • MEAN_CLUSTERS_PER_TILE

      public double MEAN_CLUSTERS_PER_TILE
      The mean number of clusters per tile.

    • SD_CLUSTERS_PER_TILE

      public double SD_CLUSTERS_PER_TILE
      The standard deviation of clusters per tile.

    • MEAN_PCT_PF_CLUSTERS_PER_TILE

      public double MEAN_PCT_PF_CLUSTERS_PER_TILE
      The mean percentage of pf clusters per tile.

    • SD_PCT_PF_CLUSTERS_PER_TILE

      public double SD_PCT_PF_CLUSTERS_PER_TILE
      The standard deviation in percentage of pf clusters per tile.

    • MEAN_PF_CLUSTERS_PER_TILE

      public double MEAN_PF_CLUSTERS_PER_TILE
      The mean number of pf clusters per tile.

    • SD_PF_CLUSTERS_PER_TILE

      public double SD_PF_CLUSTERS_PER_TILE
      The standard deviation in number of pf clusters per tile.

  • Constructor Details

    • IlluminaBasecallingMetrics

      public IlluminaBasecallingMetrics()

  • Method Details

    • toString

      public String toString()
      Overrides:
      toString in class htsjdk.samtools.metrics.MetricBase