AbstractIlluminaPositionFileReader (picard 2.18.2 API)

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

All Implemented Interfaces:

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

Direct Known Subclasses:

ClocsFileReader, LocsFileReader, PosFileReader
```
public abstract class AbstractIlluminaPositionFileReader
extends Object
implements htsjdk.samtools.util.CloseableIterator<AbstractIlluminaPositionFileReader.PositionInfo>
```
The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs. Each of these file types we read sequentially and are really concerned with iterating over the coordinates and returning them as as they would appear in a QSeq file. Therefore, this abstract base class provides the basic functionality for iterating over the values found in these files and converting them into qseq style coordinates.
Currently these readers also return lane/tile but this will be unnecessary in future releases.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

class AbstractIlluminaPositionFileReader.PositionInfo

Nested Classes
Modifier and Type	Class	Description
`class`	`AbstractIlluminaPositionFileReader.PositionInfo`

Field Summary

Fields
Modifier and Type	Field	Description
`static float`	`MAX_POS`
`static float`	`MIN_POS`	At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small negative values and see what happens.
`static String`	`S_LOCS_FILE`

Constructor Summary

Constructors
Constructor	Description
`AbstractIlluminaPositionFileReader(File file)`
`AbstractIlluminaPositionFileReader(File file, int lane, int tile)`	Use this ctor if lane and tile are not discernible from file name.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`File`	`getFile()`
`int`	`getLane()`
`int`	`getTile()`
`abstract boolean`	`hasNext()`	Return true if the file has more elements to return, false otherwise
`protected abstract String`	`makeExceptionMsg()`	Create a string that will be included in any NoSuchElementException thrown by the next() method
`AbstractIlluminaPositionFileReader.PositionInfo`	`next()`	Return the next set of coordinates in a given file.
`void`	`remove()`
`protected abstract AbstractIlluminaPositionFileReader.PositionInfo`	`unsafeNextInfo()`	Returns the next position info.

Methods inherited from interface htsjdk.samtools.util.CloseableIterator
close, stream, toList

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

- Field Detail
  - MAX_POS
```
public static final float MAX_POS
```
    See Also:
    
    Constant Field Values
  - MIN_POS
```
public static final float MIN_POS
```
    At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small negative values and see what happens.
    
    See Also:
    
    Constant Field Values
  - S_LOCS_FILE
```
public static final String S_LOCS_FILE
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - AbstractIlluminaPositionFileReader
```
public AbstractIlluminaPositionFileReader(File file)
```
  - AbstractIlluminaPositionFileReader
```
public AbstractIlluminaPositionFileReader(File file,
                                          int lane,
                                          int tile)
```
    Use this ctor if lane and tile are not discernible from file name.
    
    Parameters:
    
    file - The position file to read.
    
    lane - The lane to read positions for.
    
    tile - The tile to read positions for.
- Method Detail
  - getTile
```
public int getTile()
```
  - getLane
```
public int getLane()
```
  - getFile
```
public File getFile()
```
  - next
```
public final AbstractIlluminaPositionFileReader.PositionInfo next()
```
    Return the next set of coordinates in a given file.
    
    Specified by:
    
    next in interface Iterator<AbstractIlluminaPositionFileReader.PositionInfo>
  - unsafeNextInfo
```
protected abstract AbstractIlluminaPositionFileReader.PositionInfo unsafeNextInfo()
```
    Returns the next position info. Implementations of this method do not need to call hasNext since it is called in next()
  - makeExceptionMsg
```
protected abstract String makeExceptionMsg()
```
    Create a string that will be included in any NoSuchElementException thrown by the next() method
  - hasNext
```
public abstract boolean hasNext()
```
    Return true if the file has more elements to return, false otherwise
    
    Specified by:
    
    hasNext in interface Iterator<AbstractIlluminaPositionFileReader.PositionInfo>
  - remove
```
public void remove()
```
    Specified by:
    
    remove in interface Iterator<AbstractIlluminaPositionFileReader.PositionInfo>

Class AbstractIlluminaPositionFileReader

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

Methods inherited from interface java.util.Iterator

Methods inherited from class java.lang.Object

Field Detail

MAX_POS

MIN_POS

S_LOCS_FILE

Constructor Detail

AbstractIlluminaPositionFileReader

AbstractIlluminaPositionFileReader

Method Detail

getTile

getLane

getFile

next

unsafeNextInfo

makeExceptionMsg

hasNext

remove