Package picard.illumina.parser
Class PosParser
- java.lang.Object
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- picard.illumina.parser.PerTileParser<picard.illumina.parser.PositionalData>
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- picard.illumina.parser.PosParser
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- All Implemented Interfaces:
Iterator<picard.illumina.parser.PositionalData>
public class PosParser extends PerTileParser<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
Constructors Constructor Description PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int startingTile, IlluminaFileUtil.SupportedIlluminaFormat fileType)
PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, IlluminaFileUtil.SupportedIlluminaFormat fileType)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected htsjdk.samtools.util.CloseableIterator<picard.illumina.parser.PositionalData>
makeTileIterator(File file)
Make an CloseableIteratorbased on the given file and fileType specified at construction. Set<IlluminaDataType>
supportedTypes()
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Methods inherited from class picard.illumina.parser.PerTileParser
close, getTileOfNextCluster, hasNext, maybeAdvance, next, remove, seekToTile, verifyData
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Detail
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PosParser
public PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, IlluminaFileUtil.SupportedIlluminaFormat fileType)
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PosParser
public PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int startingTile, IlluminaFileUtil.SupportedIlluminaFormat fileType)
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Method Detail
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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
public Set<IlluminaDataType> supportedTypes()
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