public class MultiTileBclFileUtil extends ParameterizedFileUtil
base, DefaultSkipEmptyFiles, extension, faker, lane, matchPattern, PER_TILE_PATTERN_STRING, skipEmptyFiles, tiles
Modifier and Type | Method and Description |
---|---|
java.util.List<java.lang.String> |
fakeFiles(java.util.List<java.lang.Integer> expectedTiles,
int[] expectedCycles,
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.CycleIlluminaFileMap |
getFiles(java.util.List<java.lang.Integer> tiles,
int[] cycles) |
java.util.List<java.lang.Integer> |
getTiles()
Return a list of all tiles available for this file format and run
|
java.util.List<java.lang.String> |
verify(java.util.List<java.lang.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, makeLaneTileRegex
public picard.illumina.parser.CycleIlluminaFileMap getFiles(java.util.List<java.lang.Integer> tiles, int[] cycles)
public boolean filesAvailable()
ParameterizedFileUtil
filesAvailable
in class ParameterizedFileUtil
public java.util.List<java.lang.Integer> getTiles()
ParameterizedFileUtil
getTiles
in class ParameterizedFileUtil
public java.util.List<java.lang.String> verify(java.util.List<java.lang.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 java.util.List<java.lang.String> fakeFiles(java.util.List<java.lang.Integer> expectedTiles, int[] expectedCycles, IlluminaFileUtil.SupportedIlluminaFormat format)
ParameterizedFileUtil
fakeFiles
in class ParameterizedFileUtil
expectedTiles
- An ordered list of tile numbersexpectedCycles
- An ordered list of cycle numbers that may contain gapsformat
- The format of the files that are to be faked