Class PerTilePerCycleFileUtil

    • Constructor Detail

      • PerTilePerCycleFileUtil

        public PerTilePerCycleFileUtil​(String extension,
                                       File base,
                                       FileFaker faker,
                                       int lane)
    • Method Detail

      • getPerTilePerCycleFiles

        protected picard.illumina.parser.CycleIlluminaFileMap getPerTilePerCycleFiles()
        For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCycles
        Returns:
        A CycleIlluminaFileMap with the listed (or all) tiles for at least expectedCycles number of cycles(or total available cycles if expectedCycles is null)
      • getFiles

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

        public picard.illumina.parser.CycleIlluminaFileMap getFiles​(List<Integer> tiles)
      • getFiles

        public picard.illumina.parser.CycleIlluminaFileMap getFiles​(int[] cycles)
        Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in. Any cycles that are missing cycle files or directories will be removed from the cycle list that is kept.
        Parameters:
        cycles - Cycles that should be present in the output CycleIlluminaFileMap
        Returns:
        A CycleIlluminaFileMap with all available tiles but at most the cycles passed in by the cycles parameter
      • getFiles

        public picard.illumina.parser.CycleIlluminaFileMap getFiles​(List<Integer> tiles,
                                                                    int[] cycles)
        Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).
        Parameters:
        cycles - Cycles that should be present in the output CycleIlluminaFileMap
        Returns:
        A CycleIlluminaFileMap with at most the tiles/cycles listed in the parameters
      • getDetectedCycles

        public Set<Integer> getDetectedCycles()
      • getTiles

        public List<Integer> getTiles()
        Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files. The same number of tiles is expected in each cycle dir.
        Overrides:
        getTiles in class ParameterizedFileUtil
        Returns:
        A list of tile integers for all tiles available
      • 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
      • getCycleFromDir

        public static int getCycleFromDir​(File tempCycleDir)