picard.illumina.parser

Class PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>

java.lang.Object

picard.illumina.parser.PerTileParser<ILLUMINA_DATA>

Direct Known Subclasses:

PosParser

public abstract class PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>
extends java.lang.Object

Abstract base class for Parsers that open a single tile file at a time and iterate through them.

Constructor Summary

Constructors

Constructor and Description
PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles)
PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int nextTile)

Method Summary

Modifier and Type	Method and Description
void	close()
int	getTileOfNextCluster() Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next.
boolean	hasNext() Is there a DATA_TYPE object for another cluster remaining.
protected abstract htsjdk.samtools.util.CloseableIterator<ILLUMINA_DATA>	makeTileIterator(java.io.File nextTileFile) Factory method for the iterator of each tile
void	maybeAdvance()
ILLUMINA_DATA	next() Read the next read's set of data and set it into the provided data object.
void	remove()
void	seekToTile(int oneBasedTileNumber) Jump so that the next record returned will be from the specified tile.
java.util.Set<IlluminaDataType>	supportedTypes() The DataTypes that this parser can provide
void	verifyData(java.util.List<java.lang.Integer> tiles, int[] cycles) Given the expected tiles and cycles for this run, make sure this parser can provide data for all tiles/cycles or throws an exception if it's missing any required data or data structures it relies on do not disagree with the provided tiles/cycles

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

PerTileParser

public PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles)

PerTileParser

public PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles,
                     int nextTile)

Method Detail

makeTileIterator

protected abstract htsjdk.samtools.util.CloseableIterator<ILLUMINA_DATA> makeTileIterator(java.io.File nextTileFile)

Factory method for the iterator of each tile

getTileOfNextCluster

public int getTileOfNextCluster()

Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next. This might force us to advance to the next file (as it will contains the data for the next) tile/ILLUMINA_DATA object.

Returns:

tile number for the next ILLUMINA_DATA object to be returned

seekToTile

public void seekToTile(int oneBasedTileNumber)

Jump so that the next record returned will be from the specified tile.

maybeAdvance

public void maybeAdvance()

next

public ILLUMINA_DATA next()

Read the next read's set of data and set it into the provided data object. The object must have the appropriate IlluminaEndData objects set into it for first end, second end, barcode.

remove

public void remove()

hasNext

public boolean hasNext()

Is there a DATA_TYPE object for another cluster remaining.

Returns:

TRUE if there is a DATA_TYPE object for the next cluster that can be provided by next

close

public void close()

verifyData

public void verifyData(java.util.List<java.lang.Integer> tiles,
                       int[] cycles)

Given the expected tiles and cycles for this run, make sure this parser can provide data for all tiles/cycles or throws an exception if it's missing any required data or data structures it relies on do not disagree with the provided tiles/cycles

Parameters:

tiles - The number of tiles in the current run

cycles - The number of cycles in the current run

supportedTypes

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

The DataTypes that this parser can provide