Package picard.illumina.parser
Class MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
- java.lang.Object
-
- picard.illumina.parser.ParameterizedFileUtil
-
- picard.illumina.parser.MultiTileFileUtil<OUTPUT_RECORD>
-
public abstract class MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> extends ParameterizedFileUtil
For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_.bci file can be used to figure out where each tile starts and ends.
-
-
Field Summary
Fields Modifier and Type Field Description protected File
bci
protected File
dataFile
protected TileIndex
tileIndex
-
Fields inherited from class picard.illumina.parser.ParameterizedFileUtil
base, DefaultSkipEmptyFiles, extension, faker, lane, matchPattern, PER_TILE_PATTERN_STRING, skipEmptyFiles, tiles
-
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description List<String>
fakeFiles(List<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 availableList<Integer>
getTiles()
Return a list of all tiles available for this file format and runList<String>
verify(List<Integer> expectedTiles, int[] expectedCycles)
expectedCycles are not checked in this implementation.-
Methods inherited from class picard.illumina.parser.ParameterizedFileUtil
checkTileCount, escapePeriods, fileToTile, getRunFile, getTiledFiles, 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
-
getTiles
public List<Integer> getTiles()
Description copied from class:ParameterizedFileUtil
Return a list of all tiles available for this file format and run- Overrides:
getTiles
in classParameterizedFileUtil
- Returns:
- A List of tile integers
-
verify
public List<String> verify(List<Integer> expectedTiles, int[] expectedCycles)
expectedCycles are not checked in this implementation.- 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[] expectedCycles, 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 numbersexpectedCycles
- 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
-
-