LocsFileReader (picard 2.24.1 API)

java.lang.Object
- picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- - picard.illumina.parser.readers.LocsFileReader

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<AbstractIlluminaPositionFileReader.PositionInfo>, Closeable, AutoCloseable, 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, S_LOCS_FILE

Constructor Summary

Constructors
Constructor Description

LocsFileReader(File file)

LocsFileReader(File file, int lane, int tile)

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
`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 htsjdk.samtools.util.CloseableIterator
stream, toList

Methods inherited from interface java.util.Iterator
forEachRemaining

- Constructor Detail
  - LocsFileReader
```
public LocsFileReader(File file)
```
  - LocsFileReader
```
public LocsFileReader(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 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()
```
  - skipRecords
```
public void skipRecords(int numToSkip)
```