Package picard.illumina.parser
Class MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
java.lang.Object
picard.illumina.parser.MultiTileParser<OUTPUT_RECORD>
- Type Parameters:
OUTPUT_RECORD
- The kind of record to be returned (as opposed to the type of the record stored in the file).
- All Implemented Interfaces:
Iterator<OUTPUT_RECORD>
- Direct Known Subclasses:
MultiTileFilterParser
,MultiTileLocsParser
public abstract class MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
extends Object
Abstract class for files with fixed-length records for multiple tiles, e.g. .locs and .filter files.
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Constructor Summary
ConstructorsConstructorDescriptionMultiTileParser
(TileIndex tileIndex, List<Integer> requestedTiles, Set<IlluminaDataType> supportedTypes) -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
int
boolean
hasNext()
next()
void
remove()
void
seekToTile
(int oneBasedTileNumber) void
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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MultiTileParser
public MultiTileParser(TileIndex tileIndex, List<Integer> requestedTiles, Set<IlluminaDataType> supportedTypes) - Parameters:
tileIndex
- Enables conversion from tile number to record number in this file.requestedTiles
- Iterate over these tile numbers, which must be in ascending order.supportedTypes
- The data types(s) that are provided by this file type, used to decide what file types to read.
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Method Details
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seekToTile
public void seekToTile(int oneBasedTileNumber) -
next
- Specified by:
next
in interfaceIterator<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
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hasNext
public boolean hasNext()- Specified by:
hasNext
in interfaceIterator<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
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getTileOfNextCluster
public int getTileOfNextCluster() -
verifyData
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supportedTypes
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remove
public void remove()- Specified by:
remove
in interfaceIterator<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
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close
void close()
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