Field Detail

• CYCLE_CONTAINING_TILE_METRICS

  public static String CYCLE_CONTAINING_TILE_METRICS

  The cycle directory that contain the tile metrics output. (Cycle 25 for NovaSeq)

• 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

• renderTileMetricsFileFromBasecallingDirectory

  public static File renderTileMetricsFileFromBasecallingDirectory​(File illuminaRunDirectory,
                                                                   boolean isNovaSeq)

  Returns the path to the TileMetrics file given the basecalling directory.

• parseTileMetrics

  public static Collection<Tile> parseTileMetrics​(File tileMetricsOutFile,
                                                  Map<Integer,File> phasingMetricsFiles,
                                                  ReadStructure readStructure,
                                                  htsjdk.samtools.ValidationStringency validationStringency)
                                           throws FileNotFoundException

  Throws:

  FileNotFoundException

• parseTileMetrics

  public static Collection<Tile> parseTileMetrics​(File tileMetricsOutFile,
                                                  ReadStructure readStructure,
                                                  htsjdk.samtools.ValidationStringency validationStringency)
                                           throws FileNotFoundException

  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)

  Throws:

  FileNotFoundException

• renderPhasingMetricsFilesFromBasecallingDirectory

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