picard.illumina.parser

Class PosParser

java.lang.Object

picard.illumina.parser.PerTileParser<picard.illumina.parser.PositionalData>

picard.illumina.parser.PosParser

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.

Constructor Summary

Constructors

Constructor and Description
PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, IlluminaFileUtil.SupportedIlluminaFormat fileType)
PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int startingTile, IlluminaFileUtil.SupportedIlluminaFormat fileType)

Method Summary

Modifier and Type	Method and Description
protected htsjdk.samtools.util.CloseableIterator<picard.illumina.parser.PositionalData>	makeTileIterator(java.io.File file) Make an CloseableIterator based on the given file and fileType specified at construction.
java.util.Set<IlluminaDataType>	supportedTypes()

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

Constructor Detail

PosParser

public PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles,
                 IlluminaFileUtil.SupportedIlluminaFormat fileType)

PosParser

public PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles,
                 int startingTile,
                 IlluminaFileUtil.SupportedIlluminaFormat fileType)

Method Detail

makeTileIterator

protected htsjdk.samtools.util.CloseableIterator<picard.illumina.parser.PositionalData> makeTileIterator(java.io.File file)

Make an CloseableIterator based 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 class PerTileParser<picard.illumina.parser.PositionalData>

Parameters:

file - A file for the current tile being parsed

Returns:

An iterator over the PositionalData in that file.

supportedTypes

public java.util.Set<IlluminaDataType> supportedTypes()