Class PerTileFileUtil

    • Constructor Detail

      • 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 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
      • 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