picard.illumina.parser.readers

Class PosFileReader

java.lang.Object

picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

picard.illumina.parser.readers.PosFileReader

All Implemented Interfaces:

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

public class PosFileReader
extends AbstractIlluminaPositionFileReader

The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively. pos files store position data for successive clusters in tabbed delimited coordinated pairs, 1 per file row e.g.: xPos1\tyPos1 xPos2\tyPos2 102.0\t303.3 ... xPosn-1\yPosn-1 xPosn\yPosn Where n = the total number of clusters (and therefore lines) in the file.

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
PosFileReader(java.io.File posFile)

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() Read a line of text and parse it into two float values, create a PositionInfo and return it

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

PosFileReader

public PosFileReader(java.io.File posFile)

Method Detail

unsafeNextInfo

protected AbstractIlluminaPositionFileReader.PositionInfo unsafeNextInfo()

Read a line of text and parse it into two float values, create a PositionInfo and return it

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()