Class PerTilePerCycleFileUtil

java.lang.Object
picard.illumina.parser.ParameterizedFileUtil
picard.illumina.parser.PerTilePerCycleFileUtil

public class PerTilePerCycleFileUtil extends ParameterizedFileUtil
  • Constructor Details

    • PerTilePerCycleFileUtil

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

    • 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)