Package picard.illumina.parser
Class PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>
- java.lang.Object
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- picard.illumina.parser.PerTileParser<ILLUMINA_DATA>
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Constructor Summary
Constructors Constructor Description PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles)
PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int nextTile)
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description void
close()
int
getTileOfNextCluster()
Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next.boolean
hasNext()
protected abstract htsjdk.samtools.util.CloseableIterator<ILLUMINA_DATA>
makeTileIterator(File nextTileFile)
Factory method for the iterator of each tilevoid
maybeAdvance()
ILLUMINA_DATA
next()
void
remove()
void
seekToTile(int oneBasedTileNumber)
Set<IlluminaDataType>
supportedTypes()
The DataTypes that this parser can providevoid
verifyData(List<Integer> tiles, int[] cycles)
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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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makeTileIterator
protected abstract htsjdk.samtools.util.CloseableIterator<ILLUMINA_DATA> makeTileIterator(File nextTileFile)
Factory method for the iterator of each tile
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getTileOfNextCluster
public int getTileOfNextCluster()
Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next. This might force us to advance to the next file (as it will contains the data for the next) tile/ILLUMINA_DATA object.- Returns:
- tile number for the next ILLUMINA_DATA object to be returned
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seekToTile
public void seekToTile(int oneBasedTileNumber)
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maybeAdvance
public void maybeAdvance()
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next
public ILLUMINA_DATA next()
- Specified by:
next
in interfaceIterator<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>
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remove
public void remove()
- Specified by:
remove
in interfaceIterator<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>
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hasNext
public boolean hasNext()
- Specified by:
hasNext
in interfaceIterator<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>
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close
public void close()
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supportedTypes
public abstract Set<IlluminaDataType> supportedTypes()
The DataTypes that this parser can provide
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