Package picard.illumina.parser
Class PerTileFileUtil
java.lang.Object
picard.illumina.parser.ParameterizedFileUtil
picard.illumina.parser.PerTileFileUtil
- Direct Known Subclasses:
PerTileOrPerRunFileUtil
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Field Summary
Fields inherited from class picard.illumina.parser.ParameterizedFileUtil
base, DefaultSkipEmptyFiles, extension, faker, lane, matchPattern, PER_TILE_PATTERN_STRING, skipEmptyFiles, tiles
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Constructor Summary
ConstructorsConstructorDescriptionPerTileFileUtil
(String extension, File base, FileFaker faker, int lane) PerTileFileUtil
(String extension, File base, FileFaker faker, int lane, boolean skipEmptyFiles) -
Method Summary
Modifier and TypeMethodDescriptionfakeFiles
(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
Determine whether or not files are availablepicard.illumina.parser.IlluminaFileMap
getFiles()
picard.illumina.parser.IlluminaFileMap
Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed filesMethods inherited from class picard.illumina.parser.ParameterizedFileUtil
checkTileCount, escapePeriods, fileToTile, getRunFile, getTiledFiles, getTiles, makeBarcodeRegex, makeLaneTileRegex, setTiles, setTilesForPerRunFile
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Constructor Details
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PerTileFileUtil
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PerTileFileUtil
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Method Details
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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
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getFiles
public picard.illumina.parser.IlluminaFileMap getFiles() -
getFiles
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verify
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
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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
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