public abstract class MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> extends ParameterizedFileUtil
Modifier and Type | Field and Description |
---|---|
protected java.io.File |
bci |
protected java.io.File |
dataFile |
protected TileIndex |
tileIndex |
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
|
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)
expectedCycles are not checked in this implementation.
|
fileToTile, getTiledFiles, makeLaneTileRegex
protected final java.io.File bci
protected TileIndex tileIndex
protected java.io.File dataFile
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)
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