Package picard.illumina.parser
Class PosParser
java.lang.Object
picard.illumina.parser.PerTileParser<picard.illumina.parser.PositionalData>
picard.illumina.parser.PosParser
- All Implemented Interfaces:
Iterator<picard.illumina.parser.PositionalData>
PosParser parses multiple files formatted as one of the three file formats that contain position information
only (pos, locs, and clocs). This parser takes a map from tilesToFiles and a FileType enum value indicating
whether or not these are POS,LOCS, or CLOCS files. The only client classes to this class should be IlluminaDataProvider
and test classes. Check out AbstractIlluminaFileReader, PosFileReader, LocsFileReader, and ClocsFileReader for
more information on Position related illumina files.
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Constructor Summary
ConstructorsConstructorDescriptionPosParser
(picard.illumina.parser.IlluminaFileMap tilesToFiles, int startingTile, IlluminaFileUtil.SupportedIlluminaFormat fileType) PosParser
(picard.illumina.parser.IlluminaFileMap tilesToFiles, IlluminaFileUtil.SupportedIlluminaFormat fileType) -
Method Summary
Modifier and TypeMethodDescriptionprotected htsjdk.samtools.util.CloseableIterator<picard.illumina.parser.PositionalData>
makeTileIterator
(File file) Make an CloseableIteratorbased on the given file and fileType specified at construction. Methods inherited from class picard.illumina.parser.PerTileParser
close, getTileOfNextCluster, hasNext, maybeAdvance, next, remove, seekToTile, verifyData
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Details
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PosParser
public PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, IlluminaFileUtil.SupportedIlluminaFormat fileType) -
PosParser
public PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int startingTile, IlluminaFileUtil.SupportedIlluminaFormat fileType)
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Method Details
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makeTileIterator
protected htsjdk.samtools.util.CloseableIterator<picard.illumina.parser.PositionalData> makeTileIterator(File file) Make an CloseableIteratorbased on the given file and fileType specified at construction. This method wraps a reader in an iterator that converts it's output to the output format expected by IlluminaDataProvider (PositionalData). - Specified by:
makeTileIterator
in classPerTileParser<picard.illumina.parser.PositionalData>
- Parameters:
file
- A file for the current tile being parsed- Returns:
- An iterator over the PositionalData in that file.
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supportedTypes
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