PosParser (picard 2.18.2 API)

java.lang.Object
- picard.illumina.parser.PerTileParser<picard.illumina.parser.PositionalData>
- - picard.illumina.parser.PosParser

All Implemented Interfaces:

Iterator<picard.illumina.parser.PositionalData>
```
public class PosParser
extends PerTileParser<picard.illumina.parser.PositionalData>
```
PosParser parses multiple files formatted as one of the three file formats that contain position information only (pos, locs, and clocs). This parser takes a map from tilesToFiles and a FileType enum value indicating whether or not these are POS,LOCS, or CLOCS files. The only client classes to this class should be IlluminaDataProvider and test classes. Check out AbstractIlluminaFileReader, PosFileReader, LocsFileReader, and ClocsFileReader for more information on Position related illumina files.

Constructor Summary

Constructors
Constructor	Description
`PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int startingTile, IlluminaFileUtil.SupportedIlluminaFormat fileType)`
`PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, IlluminaFileUtil.SupportedIlluminaFormat fileType)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected htsjdk.samtools.util.CloseableIterator<picard.illumina.parser.PositionalData>`	`makeTileIterator(File file)`	Make an CloseableIterator based on the given file and fileType specified at construction.
`Set<IlluminaDataType>`	`supportedTypes()`

Methods inherited from interface java.util.Iterator
forEachRemaining

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class picard.illumina.parser.PerTileParser
close, getTileOfNextCluster, hasNext, maybeAdvance, next, remove, seekToTile, verifyData

Constructor Detail

PosParser

public PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles,
                 IlluminaFileUtil.SupportedIlluminaFormat fileType)

PosParser

public PosParser(picard.illumina.parser.IlluminaFileMap tilesToFiles,
                 int startingTile,
                 IlluminaFileUtil.SupportedIlluminaFormat fileType)

Method Detail
- makeTileIterator
```
protected htsjdk.samtools.util.CloseableIterator<picard.illumina.parser.PositionalData> makeTileIterator(File file)
```
  Make an CloseableIterator based on the given file and fileType specified at construction. This method wraps a reader in an iterator that converts it's output to the output format expected by IlluminaDataProvider (PositionalData).
  
  Specified by:
  
  makeTileIterator in class PerTileParser<picard.illumina.parser.PositionalData>
  
  Parameters:
  
  file - A file for the current tile being parsed
  
  Returns:
  
  An iterator over the PositionalData in that file.
- supportedTypes
```
public Set<IlluminaDataType> supportedTypes()
```

Class PosParser

Constructor Summary

Method Summary

Methods inherited from interface java.util.Iterator

Methods inherited from class java.lang.Object

Methods inherited from class picard.illumina.parser.PerTileParser

Constructor Detail

PosParser

PosParser

Method Detail

makeTileIterator

supportedTypes