Package picard.illumina.parser
Class MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
java.lang.Object
picard.illumina.parser.ParameterizedFileUtil
picard.illumina.parser.MultiTileFileUtil<OUTPUT_RECORD>
public abstract class MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
extends ParameterizedFileUtil
For file types for which there is one file per lane, with fixed record size, and all the tiles in it,
so the s_.bci file can be used to figure out where each tile starts and ends.
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Field Summary
FieldsFields 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
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 availablegetTiles()
Return a list of all tiles available for this file format and runexpectedCycles are not checked in this implementation.Methods inherited from class picard.illumina.parser.ParameterizedFileUtil
checkTileCount, escapePeriods, fileToTile, getRunFile, getTiledFiles, makeBarcodeRegex, makeLaneTileRegex, setTiles, setTilesForPerRunFile
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Field Details
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bci
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tileIndex
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dataFile
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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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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
expectedCycles are not checked in this implementation.- 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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