Package picard.illumina.parser
Class PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>
java.lang.Object
picard.illumina.parser.PerTileParser<ILLUMINA_DATA>
- All Implemented Interfaces:
Iterator<ILLUMINA_DATA>
- Direct Known Subclasses:
PosParser
public abstract class PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>
extends Object
Abstract base class for Parsers that open a single tile file at a time and iterate through them.
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Constructor Summary
ConstructorsConstructorDescriptionPerTileParser
(picard.illumina.parser.IlluminaFileMap tilesToFiles) PerTileParser
(picard.illumina.parser.IlluminaFileMap tilesToFiles, int nextTile) -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
int
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
next()
void
remove()
void
seekToTile
(int oneBasedTileNumber) The DataTypes that this parser can providevoid
verifyData
(List<Integer> tiles, int[] cycles) Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Details
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PerTileParser
public PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles) -
PerTileParser
public PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int nextTile)
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Method Details
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makeTileIterator
protected abstract htsjdk.samtools.util.CloseableIterator<ILLUMINA_DATA> makeTileIterator(File nextTileFile) Factory method for the iterator of each tile -
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) -
maybeAdvance
public void maybeAdvance() -
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() -
verifyData
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supportedTypes
Set<IlluminaDataType> supportedTypes()The DataTypes that this parser can provide
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