Package picard.illumina.parser
Class PerTileOrPerRunFileUtil
java.lang.Object
picard.illumina.parser.ParameterizedFileUtil
picard.illumina.parser.PerTileFileUtil
picard.illumina.parser.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
ConstructorsConstructorDescriptionPerTileOrPerRunFileUtil
(String extension, File base, FileFaker faker, int lane) -
Method Summary
Modifier and TypeMethodDescriptionboolean
boolean
Determine whether or not files are availablevoid
setTilesForPerRunFile
(List<Integer> tiles) 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.PerTileFileUtil
fakeFiles, getFiles, getFiles
Methods inherited from class picard.illumina.parser.ParameterizedFileUtil
escapePeriods, fileToTile, getRunFile, getTiledFiles, getTiles, makeBarcodeRegex, makeLaneTileRegex, setTiles
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Constructor Details
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PerTileOrPerRunFileUtil
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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- Overrides:
filesAvailable
in classPerTileFileUtil
- Returns:
- return true if files are found matching this types pattern, false otherwise
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setTilesForPerRunFile
- Overrides:
setTilesForPerRunFile
in classParameterizedFileUtil
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checkTileCount
public boolean checkTileCount()- Overrides:
checkTileCount
in classParameterizedFileUtil
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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- Overrides:
verify
in classPerTileFileUtil
- 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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