public class PerTileFileUtil extends ParameterizedFileUtil
base, DefaultSkipEmptyFiles, extension, faker, lane, matchPattern, PER_TILE_PATTERN_STRING, skipEmptyFiles, tiles
Constructor and Description |
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PerTileFileUtil(String extension,
File base,
FileFaker faker,
int lane) |
PerTileFileUtil(String extension,
File base,
FileFaker faker,
int lane,
boolean skipEmptyFiles) |
Modifier and Type | Method and Description |
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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 available
|
picard.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
|
fileToTile, getTiledFiles, getTiles, makeLaneTileRegex
public boolean filesAvailable()
ParameterizedFileUtil
filesAvailable
in class ParameterizedFileUtil
public picard.illumina.parser.IlluminaFileMap getFiles()
public List<String> verify(List<Integer> expectedTiles, int[] expectedCycles)
ParameterizedFileUtil
verify
in class ParameterizedFileUtil
expectedTiles
- An ordered list of tile numbersexpectedCycles
- An ordered list of cycle numbers that may contain gapspublic List<String> fakeFiles(List<Integer> expectedTiles, int[] cycles, IlluminaFileUtil.SupportedIlluminaFormat format)
ParameterizedFileUtil
fakeFiles
in class ParameterizedFileUtil
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