Package picard.illumina

Class IlluminaBasecallingMetrics

  • 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 Detail

      • 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 Detail

      • IlluminaBasecallingMetrics

        public IlluminaBasecallingMetrics()

    • Method Detail

      • toString

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