Class TileMetricsUtil


  • public class TileMetricsUtil
    extends Object
    Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
    • Field Detail

      • INTEROP_SUBDIRECTORY_NAME

        public static String INTEROP_SUBDIRECTORY_NAME
        The path to the directory containing the tile metrics file relative to the basecalling directory.
      • TILE_METRICS_OUT_FILE_NAME

        public static String TILE_METRICS_OUT_FILE_NAME
        The expected name of the tile metrics output file.
    • Constructor Detail

      • TileMetricsUtil

        public TileMetricsUtil()
    • Method Detail

      • findTileMetricsFiles

        public static List<File> findTileMetricsFiles​(File illuminaRunDirectory,
                                                      int numCycles)
        Finds all of the tile metrics files for a given run directory and cycle count.
        Parameters:
        illuminaRunDirectory - The run directory
        numCycles - The number of cycle directories to check.
        Returns:
        A list of all tile metrics files.
      • parseTileMetrics

        public static Collection<Tile> parseTileMetrics​(File tileMetricsOutFile,
                                                        ReadStructure readStructure,
                                                        htsjdk.samtools.ValidationStringency validationStringency)
        Returns an unmodifiable collection of tile data read from the provided file. For each tile we will extract: - lane number - tile number - density - cluster ID - Phasing & Prephasing for first template read (if available) - Phasing & Prephasing for second template read (if available)
      • renderPhasingMetricsFilesFromBasecallingDirectory

        public static Map<Integer,​File> renderPhasingMetricsFilesFromBasecallingDirectory​(File illuminaRunDirectory)