Package picard.illumina.parser
Class MultiTileBclFileUtil
- java.lang.Object
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- picard.illumina.parser.ParameterizedFileUtil
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- picard.illumina.parser.MultiTileBclFileUtil
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public class MultiTileBclFileUtil extends ParameterizedFileUtil
NextSeq-style bcl's have all tiles for a cycle in a single file.
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Field Summary
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Fields inherited from class picard.illumina.parser.ParameterizedFileUtil
base, DefaultSkipEmptyFiles, extension, faker, lane, matchPattern, PER_TILE_PATTERN_STRING, skipEmptyFiles, tiles
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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 availablepicard.illumina.parser.CycleIlluminaFileMap
getFiles(List<Integer> tiles, int[] cycles)
List<Integer>
getTiles()
Return a list of all tiles available for this file format and runList<String>
verify(List<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-
Methods inherited from class picard.illumina.parser.ParameterizedFileUtil
checkTileCount, escapePeriods, fileToTile, getRunFile, getTiledFiles, makeBarcodeRegex, makeLaneTileRegex, setTiles, setTilesForPerRunFile
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Method Detail
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getFiles
public picard.illumina.parser.CycleIlluminaFileMap getFiles(List<Integer> tiles, int[] cycles)
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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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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
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verify
public List<String> verify(List<Integer> expectedTiles, int[] expectedCycles)
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[] 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
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