picard.illumina.parser.readers

Class AbstractIlluminaPositionFileReader

java.lang.Object

picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

All Implemented Interfaces:

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

Direct Known Subclasses:

ClocsFileReader, LocsFileReader, PosFileReader

public abstract class AbstractIlluminaPositionFileReader
extends java.lang.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 and Description
class	AbstractIlluminaPositionFileReader.PositionInfo

Field Summary

Fields

Modifier and Type	Field and 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.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
java.io.File	getFile()
int	getLane()
int	getTile()
abstract boolean	hasNext() Return true if the file has more elements to return, false otherwise
protected abstract java.lang.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 class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

close, stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

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

Constructor Detail

AbstractIlluminaPositionFileReader

public AbstractIlluminaPositionFileReader(java.io.File file)

AbstractIlluminaPositionFileReader

public AbstractIlluminaPositionFileReader(java.io.File file,
                                          int lane,
                                          int tile)

Use this ctor if lane and tile are not discernible from file name.

Parameters:

file -

lane -

tile -

Method Detail

getTile

public int getTile()

getLane

public int getLane()

getFile

public java.io.File getFile()

next

public final AbstractIlluminaPositionFileReader.PositionInfo next()

Return the next set of coordinates in a given file.

Specified by:

next in interface java.util.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 java.lang.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 java.util.Iterator<AbstractIlluminaPositionFileReader.PositionInfo>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<AbstractIlluminaPositionFileReader.PositionInfo>