picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

picard.illumina.parser.readers.PosFileReader

All Implemented Interfaces:: htsjdk.samtools.util.CloseableIterator<AbstractIlluminaPositionFileReader.PositionInfo>, Closeable, AutoCloseable, 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, S_LOCS_FILE
Constructor Summary

Constructors

Constructor

Description

PosFileReader(File posFile)
Method Summary

Modifier and Type

Method

Description

void

close()

boolean

hasNext()

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

protected 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 Details
- PosFileReader
  
  public PosFileReader(File posFile)
Method Details
- 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 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 Iterator<AbstractIlluminaPositionFileReader.PositionInfo>
  
  Specified by:
  
  hasNext in class AbstractIlluminaPositionFileReader
- close
  
  public void close()

Class PosFileReader

Nested Class Summary

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

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

Methods inherited from interface java.util.Iterator

Constructor Details

PosFileReader

Method Details

unsafeNextInfo

makeExceptionMsg

hasNext

close