Package picard.illumina.parser
Class PerTilePerCycleFileUtil
java.lang.Object
picard.illumina.parser.ParameterizedFileUtil
picard.illumina.parser.PerTilePerCycleFileUtil
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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
ConstructorsConstructorDescriptionPerTilePerCycleFileUtil
(String extension, File base, FileFaker faker, int lane) -
Method Summary
Modifier and TypeMethodDescriptionfakeFiles
(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
Determine whether or not files are availablestatic int
getCycleFromDir
(File tempCycleDir) picard.illumina.parser.CycleIlluminaFileMap
getFiles()
picard.illumina.parser.CycleIlluminaFileMap
getFiles
(int[] cycles) Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in.picard.illumina.parser.CycleIlluminaFileMap
picard.illumina.parser.CycleIlluminaFileMap
Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).protected picard.illumina.parser.CycleIlluminaFileMap
For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCyclesgetTiles()
Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files.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, makeBarcodeRegex, makeLaneTileRegex, setTiles, setTilesForPerRunFile
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Constructor Details
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PerTilePerCycleFileUtil
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Method Details
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getPerTilePerCycleFiles
protected picard.illumina.parser.CycleIlluminaFileMap getPerTilePerCycleFiles()For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCycles- Returns:
- A CycleIlluminaFileMap with the listed (or all) tiles for at least expectedCycles number of cycles(or total available cycles if expectedCycles is null)
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getFiles
public picard.illumina.parser.CycleIlluminaFileMap getFiles() -
getFiles
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getFiles
public picard.illumina.parser.CycleIlluminaFileMap getFiles(int[] cycles) Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in. Any cycles that are missing cycle files or directories will be removed from the cycle list that is kept.- Parameters:
cycles
- Cycles that should be present in the output CycleIlluminaFileMap- Returns:
- A CycleIlluminaFileMap with all available tiles but at most the cycles passed in by the cycles parameter
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getFiles
Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).- Parameters:
cycles
- Cycles that should be present in the output CycleIlluminaFileMap- Returns:
- A CycleIlluminaFileMap with at most the tiles/cycles listed in the parameters
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getDetectedCycles
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getTiles
Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files. The same number of tiles is expected in each cycle dir.- Overrides:
getTiles
in classParameterizedFileUtil
- Returns:
- A list of tile integers for all tiles available
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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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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[] 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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getCycleFromDir
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