picard.illumina.parser.readers

Class ClocsFileReader

java.lang.Object

picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

picard.illumina.parser.readers.ClocsFileReader

All Implemented Interfaces:

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

public class ClocsFileReader
extends AbstractIlluminaPositionFileReader

The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively. clocs files store position data for successive clusters, compressed in bins as follows: Byte 0 : unused Byte 1-4 : unsigned int numBins The rest of the file consists of bins/blocks, where a bin consists of an integer indicating number of blocks, followed by that number of blocks and a block consists of an x-y coordinate pair. In otherwords: for each bin byte 1: Unsigned int numBlocks for each block: byte 1 : byte xRelativeCoordinate byte 2 : byte yRelativeCoordinate Actual x and y values are computed using the following algorithm xOffset = yOffset = 0 imageWidth = 2048 blockSize = 25 maxXbins:Int = Math.Ceiling((double)ImageWidth/(double)blockSize) for each bin: for each location: x = convert.ToSingle(xRelativeCoordinate/10f + xoffset) y = convert.toSingle(yRelativeCoordinate/10f + yoffset) if (binIndex > 0 && ((binIndex + 1) % maxXbins == 0)) { xOffset = 0; yOffset += blockSize } else xOffset += blockSize

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
ClocsFileReader(java.io.File clocsFile)

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
protected AbstractIlluminaPositionFileReader.PositionInfo	unsafeNextInfo() Grab the next set of offset values, decompress them.

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 htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

ClocsFileReader

public ClocsFileReader(java.io.File clocsFile)

Method Detail

unsafeNextInfo

protected AbstractIlluminaPositionFileReader.PositionInfo unsafeNextInfo()

Grab the next set of offset values, decompress them.

Specified by:

unsafeNextInfo in class AbstractIlluminaPositionFileReader

Returns:

the position information of the next offset values

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()