Class TileMetricsUtil

java.lang.Object
picard.illumina.parser.TileMetricsUtil

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

    • 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 Details

    • TileMetricsUtil

      public TileMetricsUtil()
  • Method Details

    • 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.
    • parseClusterRecordsFromTileMetrics

      public static Collection<Tile> parseClusterRecordsFromTileMetrics(Collection<File> tileMetricsOutFiles, Map<Integer,File> phasingMetricsFiles, ReadStructure readStructure)
    • 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)