Class MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>


  • public abstract class MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
    extends ParameterizedFileUtil
    For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_.bci file can be used to figure out where each tile starts and ends.
    • Field Detail

      • bci

        protected final File bci
      • dataFile

        protected File dataFile
    • Method Detail

      • 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)
        expectedCycles are not checked in this implementation.
        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