Package picard.illumina.parser
Class PerTilePerCycleFileUtil
- java.lang.Object
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- picard.illumina.parser.ParameterizedFileUtil
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- picard.illumina.parser.PerTilePerCycleFileUtil
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public class PerTilePerCycleFileUtil extends ParameterizedFileUtil
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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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Constructor Summary
Constructors Constructor Description PerTilePerCycleFileUtil(String extension, File base, FileFaker faker, int lane)
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Method Summary
All Methods Static 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 availablestatic int
getCycleFromDir(File tempCycleDir)
Set<Integer>
getDetectedCycles()
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
getFiles(List<Integer> tiles)
picard.illumina.parser.CycleIlluminaFileMap
getFiles(List<Integer> tiles, int[] cycles)
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
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 numCyclesList<Integer>
getTiles()
Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files.List<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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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()
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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
public picard.illumina.parser.CycleIlluminaFileMap getFiles(List<Integer> tiles, int[] cycles)
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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getTiles
public List<Integer> 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
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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getCycleFromDir
public static int getCycleFromDir(File tempCycleDir)
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