Class IlluminaFileUtil


  • public class IlluminaFileUtil
    extends Object
    General utils for dealing with IlluminaFiles as well as utils for specific, support formats. This class contains utils that span across multiple Illumina files but it's primary intent was to provide support for basic file types. Each supported file type can be accessed via a factory method (makeFt). When IlluminaFileUtil is created it is parameterized by basecallDir and lane and all IlluminaFileTypes created by IlluminaFileUtil will also be parameterized in this fashion.
    • Field Detail

      • CYCLE_SUBDIRECTORY_PATTERN

        public static final Pattern CYCLE_SUBDIRECTORY_PATTERN
    • Constructor Detail

      • IlluminaFileUtil

        public IlluminaFileUtil​(File basecallDir,
                                int lane)
      • IlluminaFileUtil

        public IlluminaFileUtil​(File basecallDir,
                                File barcodeDir,
                                int lane)
    • Method Detail

      • getLane

        public int getLane()
        Return the lane we're inspecting
      • getExpectedTiles

        public List<Integer> getExpectedTiles()
        Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin
      • tileMetricsOut

        public File tileMetricsOut()
      • longLaneStr

        public static String longLaneStr​(int lane)
      • hasCbcls

        public static boolean hasCbcls​(File basecallDir,
                                       int lane)