picard.illumina.parser.readers

Class LocsFileReader

java.lang.Object

picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

picard.illumina.parser.readers.LocsFileReader

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<AbstractIlluminaPositionFileReader.PositionInfo>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<AbstractIlluminaPositionFileReader.PositionInfo>

public class LocsFileReader
extends AbstractIlluminaPositionFileReader

The locs file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively. locs files store position data for successive clusters in 4 byte float pairs, described as follows: bytes 1-4 : (int?) Version number (1) bytes 5-8 : 4 byte float equaling 1.0 bytes 9-12 : unsigned int numClusters bytes 13-16: : X coordinate of first cluster (32-bit float) bytes 17-20: : Y coordinate of first cluster (32-bit float) The remaining bytes of the file store the X and Y coordinates of the remaining clusters.

Nested Class Summary

Nested classes/interfaces inherited from class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

AbstractIlluminaPositionFileReader.PositionInfo

Field Summary

Fields inherited from class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

MAX_POS, MIN_POS

Constructor Summary

Constructors

Constructor and Description
LocsFileReader(java.io.File file)
LocsFileReader(java.io.File file, int lane, int tile)

Method Summary

Modifier and Type	Method and Description
void	close()
boolean	hasNext() Return true if the file has more elements to return, false otherwise
protected java.lang.String	makeExceptionMsg() Create a string that will be included in any NoSuchElementException thrown by the next() method
void	skipRecords(int numToSkip)
protected AbstractIlluminaPositionFileReader.PositionInfo	unsafeNextInfo() Returns the next position info.

Methods inherited from class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

getFile, getLane, getTile, next, remove

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

LocsFileReader

public LocsFileReader(java.io.File file)

LocsFileReader

public LocsFileReader(java.io.File file,
                      int lane,
                      int tile)

Method Detail

unsafeNextInfo

protected AbstractIlluminaPositionFileReader.PositionInfo unsafeNextInfo()

Description copied from class: AbstractIlluminaPositionFileReader

Returns the next position info. Implementations of this method do not need to call hasNext since it is called in next()

Specified by:

unsafeNextInfo in class AbstractIlluminaPositionFileReader

makeExceptionMsg

protected java.lang.String makeExceptionMsg()

Description copied from class: AbstractIlluminaPositionFileReader

Create a string that will be included in any NoSuchElementException thrown by the next() method

Specified by:

makeExceptionMsg in class AbstractIlluminaPositionFileReader

hasNext

public boolean hasNext()

Description copied from class: AbstractIlluminaPositionFileReader

Return true if the file has more elements to return, false otherwise

Specified by:

hasNext in interface java.util.Iterator<AbstractIlluminaPositionFileReader.PositionInfo>

Specified by:

hasNext in class AbstractIlluminaPositionFileReader

close

public void close()

skipRecords

public void skipRecords(int numToSkip)