Class PerTileFileUtil

java.lang.Object
picard.illumina.parser.ParameterizedFileUtil
picard.illumina.parser.PerTileFileUtil
Direct Known Subclasses:
PerTileOrPerRunFileUtil

public class PerTileFileUtil extends ParameterizedFileUtil
  • Constructor Details

    • PerTileFileUtil

      public PerTileFileUtil(String extension, File base, FileFaker faker, int lane)
    • PerTileFileUtil

      public PerTileFileUtil(String extension, File base, FileFaker faker, int lane, boolean skipEmptyFiles)
  • Method Details

    • filesAvailable

      public boolean filesAvailable()
      Description copied from class: ParameterizedFileUtil
      Determine whether or not files are available
      Specified by:
      filesAvailable in class ParameterizedFileUtil
      Returns:
      return true if files are found matching this types pattern, false otherwise
    • getFiles

      public picard.illumina.parser.IlluminaFileMap getFiles()
    • getFiles

      public picard.illumina.parser.IlluminaFileMap getFiles(List<Integer> tiles)
    • verify

      public List<String> verify(List<Integer> expectedTiles, int[] expectedCycles)
      Description copied from class: ParameterizedFileUtil
      Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files
      Specified by:
      verify in class ParameterizedFileUtil
      Parameters:
      expectedTiles - An ordered list of tile numbers
      expectedCycles - An ordered list of cycle numbers that may contain gaps
      Returns:
      A list of error messages for this format
    • fakeFiles

      public List<String> fakeFiles(List<Integer> expectedTiles, int[] cycles, IlluminaFileUtil.SupportedIlluminaFormat format)
      Description copied from class: ParameterizedFileUtil
      Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.
      Specified by:
      fakeFiles in class ParameterizedFileUtil
      Parameters:
      expectedTiles - An ordered list of tile numbers
      cycles - An ordered list of cycle numbers that may contain gaps
      format - The format of the files that are to be faked
      Returns:
      A list of error messages for this format