MultiTileBclFileUtil
, MultiTileFileUtil
, PerTileFileUtil
, PerTilePerCycleFileUtil
public abstract class ParameterizedFileUtil extends Object
Modifier and Type | Field | Description |
---|---|---|
protected 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.
|
protected static boolean |
DefaultSkipEmptyFiles |
|
protected String |
extension |
The file extension for this class, file extension does not have the standard meaning
in this instance.
|
protected FileFaker |
faker |
|
protected int |
lane |
|
protected Pattern |
matchPattern |
A pattern that will match files of this type for this lane
|
static String |
PER_TILE_PATTERN_STRING |
|
protected boolean |
skipEmptyFiles |
|
protected List<Integer> |
tiles |
Constructor | Description |
---|---|
ParameterizedFileUtil(boolean laneTileRegex,
String extension,
File base,
FileFaker faker,
int lane) |
|
ParameterizedFileUtil(boolean laneTileRegex,
String extension,
File base,
FileFaker faker,
int lane,
boolean skipEmptyFiles) |
|
ParameterizedFileUtil(String pattern,
String extension,
File base,
FileFaker faker,
int lane) |
Modifier and Type | Method | Description |
---|---|---|
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.
|
abstract boolean |
filesAvailable() |
Determine whether or not files are available
|
protected Integer |
fileToTile(String fileName) |
Returns only lane and tile information as PerTileFt's do not have End information.
|
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
|
List<Integer> |
getTiles() |
Return a list of all tiles available for this file format and run
|
static String |
makeLaneTileRegex(String fileNameEndPattern,
int lane) |
Return a regex string for finding Lane and Tile given a file extension pattern
|
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
|
public static final String PER_TILE_PATTERN_STRING
protected final String extension
protected Pattern matchPattern
protected final int lane
protected final File base
protected final FileFaker faker
protected static final boolean DefaultSkipEmptyFiles
protected final boolean skipEmptyFiles
public ParameterizedFileUtil(boolean laneTileRegex, String extension, File base, FileFaker faker, int lane, boolean skipEmptyFiles)
public ParameterizedFileUtil(boolean laneTileRegex, String extension, File base, FileFaker faker, int lane)
public abstract boolean filesAvailable()
public List<Integer> getTiles()
public abstract List<String> verify(List<Integer> expectedTiles, int[] expectedCycles)
expectedTiles
- An ordered list of tile numbersexpectedCycles
- An ordered list of cycle numbers that may contain gapspublic abstract List<String> fakeFiles(List<Integer> expectedTiles, int[] cycles, IlluminaFileUtil.SupportedIlluminaFormat format)
expectedTiles
- An ordered list of tile numberscycles
- An ordered list of cycle numbers that may contain gapsformat
- The format of the files that are to be fakedprotected Integer fileToTile(String fileName)
fileName
- Filename to analyze for datapublic static String makeLaneTileRegex(String fileNameEndPattern, int lane)