Package picard.illumina.parser
Class PerTileFileUtil
- java.lang.Object
-
- picard.illumina.parser.ParameterizedFileUtil
-
- picard.illumina.parser.PerTileFileUtil
-
- Direct Known Subclasses:
PerTileOrPerRunFileUtil
public class PerTileFileUtil extends ParameterizedFileUtil
-
-
Field Summary
-
Fields inherited from class picard.illumina.parser.ParameterizedFileUtil
base, DefaultSkipEmptyFiles, extension, faker, lane, matchPattern, PER_TILE_PATTERN_STRING, skipEmptyFiles, tiles
-
-
Constructor Summary
Constructors Constructor Description PerTileFileUtil(String extension, File base, FileFaker faker, int lane)
PerTileFileUtil(String extension, File base, FileFaker faker, int lane, boolean skipEmptyFiles)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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.boolean
filesAvailable()
Determine whether or not files are availablepicard.illumina.parser.IlluminaFileMap
getFiles()
picard.illumina.parser.IlluminaFileMap
getFiles(List<Integer> tiles)
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-
Methods inherited from class picard.illumina.parser.ParameterizedFileUtil
checkTileCount, escapePeriods, fileToTile, getRunFile, getTiledFiles, getTiles, makeBarcodeRegex, makeLaneTileRegex, setTiles, setTilesForPerRunFile
-
-
-
-
Method Detail
-
filesAvailable
public boolean filesAvailable()
Description copied from class:ParameterizedFileUtil
Determine whether or not files are available- Specified by:
filesAvailable
in classParameterizedFileUtil
- Returns:
- return true if files are found matching this types pattern, false otherwise
-
getFiles
public picard.illumina.parser.IlluminaFileMap getFiles()
-
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 classParameterizedFileUtil
- Parameters:
expectedTiles
- An ordered list of tile numbersexpectedCycles
- 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 classParameterizedFileUtil
- Parameters:
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 faked- Returns:
- A list of error messages for this format
-
-