Package picard.illumina.parser.readers
Class AbstractIlluminaPositionFileReader
- java.lang.Object
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- picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
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- 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.
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
AbstractIlluminaPositionFileReader.PositionInfo
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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
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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.
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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 otherwiseprotected abstract String
makeExceptionMsg()
Create a string that will be included in any NoSuchElementException thrown by the next() methodAbstractIlluminaPositionFileReader.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
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Methods inherited from interface java.util.Iterator
forEachRemaining
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Field Detail
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MAX_POS
public static final float MAX_POS
- See Also:
- Constant Field Values
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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
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S_LOCS_FILE
public static final String S_LOCS_FILE
- See Also:
- Constant Field Values
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Constructor Detail
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AbstractIlluminaPositionFileReader
public AbstractIlluminaPositionFileReader(File file)
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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.
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Method Detail
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getTile
public int getTile()
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getLane
public int getLane()
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getFile
public File getFile()
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next
public final AbstractIlluminaPositionFileReader.PositionInfo next()
Return the next set of coordinates in a given file.- Specified by:
next
in interfaceIterator<AbstractIlluminaPositionFileReader.PositionInfo>
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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()
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makeExceptionMsg
protected abstract String makeExceptionMsg()
Create a string that will be included in any NoSuchElementException thrown by the next() method
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hasNext
public abstract boolean hasNext()
Return true if the file has more elements to return, false otherwise- Specified by:
hasNext
in interfaceIterator<AbstractIlluminaPositionFileReader.PositionInfo>
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remove
public void remove()
- Specified by:
remove
in interfaceIterator<AbstractIlluminaPositionFileReader.PositionInfo>
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