PosFileReader (picard 2.26.10 API)

java.lang.Object
- 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

All Methods Instance Methods Concrete Methods
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 Detail
  - PosFileReader
```
public PosFileReader(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 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()
```