Field Detail

• PER_TILE_PATTERN_STRING

  public static final String PER_TILE_PATTERN_STRING

  See Also:

  Constant Field Values

• extension

  protected final String extension

  The file extension for this class, file extension does not have the standard meaning in this instance. It means, all the characters that come after the identifying portion of the file (after lane, tile, and end that is). So _qseq.txt and .filter are both file extensions

• matchPattern

  protected Pattern matchPattern

  A pattern that will match files of this type for this lane

• lane

  protected final int lane

• tiles

  protected List<Integer> tiles

• base

  protected final File base

  If you think of the file system as a tree, this is the deepest directory(node) on the tree that still contains all of the files for this given type (e.g. If we're talking about BCLs the directory structure is:

  BaseCall Dir | L001 | | | C1.1 C2.1 ... Cn.1 | | | bcl Files ... bclFiles

  L001 is the base because it contains every BCL file in the run (though those files are nested in other folders).

• faker

  protected final FileFaker faker

• DefaultSkipEmptyFiles

  protected static final boolean DefaultSkipEmptyFiles

  See Also:

  Constant Field Values

• skipEmptyFiles

  protected final boolean skipEmptyFiles

Constructor Detail

• ParameterizedFileUtil

  public ParameterizedFileUtil​(boolean laneTileRegex,
                               String extension,
                               File base,
                               FileFaker faker,
                               int lane,
                               boolean skipEmptyFiles)

• ParameterizedFileUtil

  public ParameterizedFileUtil​(boolean laneTileRegex,
                               String extension,
                               File base,
                               FileFaker faker,
                               int lane)

• ParameterizedFileUtil

  public ParameterizedFileUtil​(String pattern,
                               String extension,
                               File base,
                               FileFaker faker,
                               int lane)

Method Detail

• filesAvailable

  public abstract boolean filesAvailable()

  Determine whether or not files are available

  Returns:

  return true if files are found matching this types pattern, false otherwise

• getTiles

  public List<Integer> getTiles()

  Return a list of all tiles available for this file format and run

  Returns:

  A List of tile integers

• verify

  public abstract List<String> verify​(List<Integer> expectedTiles,
                                      int[] expectedCycles)

  Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files

  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 abstract List<String> fakeFiles​(List<Integer> expectedTiles,
                                         int[] cycles,
                                         IlluminaFileUtil.SupportedIlluminaFormat format)

  Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.

  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

• fileToTile

  protected Integer fileToTile​(String fileName)

  Returns only lane and tile information as PerTileFt's do not have End information.

  Parameters:

  fileName - Filename to analyze for data

  Returns:

  A LaneTile object with the discovered Lane and Tile information and a null end field.

• makeLaneTileRegex

  public static String makeLaneTileRegex​(String fileNameEndPattern,
                                         int lane)

  Return a regex string for finding Lane and Tile given a file extension pattern

• escapePeriods

  public static String escapePeriods​(String preEscaped)

  Escape the period character.

• getRunFile

  protected File getRunFile​(File baseDirectory,
                            Pattern pattern)

• getTiledFiles

  protected picard.illumina.parser.IlluminaFileMap getTiledFiles​(File baseDirectory,
                                                                 Pattern pattern)

  Return all files that match pattern of the given file type in the given base directory

• setTiles

  public void setTiles​(List<Integer> tiles)

• setTilesForPerRunFile

  public void setTilesForPerRunFile​(List<Integer> tiles)

• checkTileCount

  public boolean checkTileCount()

• makeBarcodeRegex

  public static String makeBarcodeRegex​(int lane)