Package picard.illumina.parser.readers
Class LocsFileReader
- java.lang.Object
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- picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
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- picard.illumina.parser.readers.LocsFileReader
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- 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.
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
AbstractIlluminaPositionFileReader.PositionInfo
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Field Summary
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Fields inherited from class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
MAX_POS, MIN_POS, S_LOCS_FILE
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Constructor Summary
Constructors Constructor Description LocsFileReader(File file)
LocsFileReader(File file, int lane, int tile)
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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 otherwiseprotected String
makeExceptionMsg()
Create a string that will be included in any NoSuchElementException thrown by the next() methodvoid
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
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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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Method Detail
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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 classAbstractIlluminaPositionFileReader
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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 classAbstractIlluminaPositionFileReader
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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 interfaceIterator<AbstractIlluminaPositionFileReader.PositionInfo>
- Specified by:
hasNext
in classAbstractIlluminaPositionFileReader
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close
public void close()
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skipRecords
public void skipRecords(int numToSkip)
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