Class IlluminaFileUtil

java.lang.Object
picard.illumina.parser.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 Details

    • CYCLE_SUBDIRECTORY_PATTERN

      public static final Pattern CYCLE_SUBDIRECTORY_PATTERN
  • Constructor Details

    • IlluminaFileUtil

      public IlluminaFileUtil(File basecallDir, int lane)
    • IlluminaFileUtil

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

    • getLane

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

      Given a file type, get the Parameterized File Util object associated with it
    • 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
    • getActualTiles

      public List<Integer> getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat> formats)
      Get the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the format
    • tileMetricsOut

      public File tileMetricsOut()
    • longLaneStr

      public static String longLaneStr(int lane)
    • hasCbcls

      public static boolean hasCbcls(File basecallDir, int lane)