Class CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector

  • Enclosing class:
    CollectIlluminaLaneMetrics

    public static class CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
    extends Object
    Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
    • Constructor Detail

      • IlluminaLaneMetricsCollector

        public IlluminaLaneMetricsCollector()
    • Method Detail

      • readLaneTiles

        public static Map<Integer,​? extends Collection<Tile>> readLaneTiles​(File illuminaRunDirectory,
                                                                                  ReadStructure readStructure,
                                                                                  htsjdk.samtools.ValidationStringency validationStringency,
                                                                                  int tileMetricsVersion)
        Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
      • collectLaneMetrics

        public static void collectLaneMetrics​(File runDirectory,
                                              File outputDirectory,
                                              String outputPrefix,
                                              htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,​Comparable<?>> laneMetricsFile,
                                              htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,​Comparable<?>> phasingMetricsFile,
                                              ReadStructure readStructure,
                                              String fileExtension,
                                              htsjdk.samtools.ValidationStringency validationStringency)
        Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files