Class MultiTileBclFileUtil


  • public class MultiTileBclFileUtil
    extends ParameterizedFileUtil
    NextSeq-style bcl's have all tiles for a cycle in a single file.
    • Method Detail

      • getFiles

        public picard.illumina.parser.CycleIlluminaFileMap getFiles​(List<Integer> tiles,
                                                                    int[] cycles)
      • 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
      • 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[] expectedCycles,
                                      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
        expectedCycles - 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