Package picard.illumina.parser.readers
Class PosFileReader
- java.lang.Object
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- picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
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- picard.illumina.parser.readers.PosFileReader
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- All Implemented Interfaces:
htsjdk.samtools.util.CloseableIterator<AbstractIlluminaPositionFileReader.PositionInfo>
,Closeable
,AutoCloseable
,Iterator<AbstractIlluminaPositionFileReader.PositionInfo>
public class PosFileReader extends AbstractIlluminaPositionFileReader
The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively. pos files store position data for successive clusters in tabbed delimited coordinated pairs, 1 per file row e.g.: xPos1\tyPos1 xPos2\tyPos2 102.0\t303.3 ... xPosn-1\yPosn-1 xPosn\yPosn Where n = the total number of clusters (and therefore lines) in the file.
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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 PosFileReader(File posFile)
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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() methodprotected AbstractIlluminaPositionFileReader.PositionInfo
unsafeNextInfo()
Read a line of text and parse it into two float values, create a PositionInfo and return it-
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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Constructor Detail
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PosFileReader
public PosFileReader(File posFile)
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Method Detail
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unsafeNextInfo
protected AbstractIlluminaPositionFileReader.PositionInfo unsafeNextInfo()
Read a line of text and parse it into two float values, create a PositionInfo and return it- 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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