OUTPUT_RECORD
- The kind of record to be returned (as opposed to the type of the record stored in the file).public abstract class MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
extends java.lang.Object
Constructor and Description |
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MultiTileParser(TileIndex tileIndex,
java.util.List<java.lang.Integer> requestedTiles,
java.util.Set<IlluminaDataType> supportedTypes) |
Modifier and Type | Method and Description |
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void |
close() |
int |
getTileOfNextCluster()
Get the tile for the NEXT DATA_TYPE object that will be returned by this parser.
|
boolean |
hasNext()
Is there a DATA_TYPE object for another cluster remaining.
|
OUTPUT_RECORD |
next()
Read the next read's set of data and set it into the provided data object.
|
void |
remove() |
void |
seekToTile(int oneBasedTileNumber)
Jump so that the next record returned will be from the specified tile.
|
java.util.Set<IlluminaDataType> |
supportedTypes()
The DataTypes that this parser can provide
|
void |
verifyData(java.util.List<java.lang.Integer> tiles,
int[] cycles)
Given the expected tiles and cycles for this run, make sure this parser can provide data for
all tiles/cycles or throws an exception if it's missing any required data or data structures
it relies on do not disagree with the provided tiles/cycles
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public MultiTileParser(TileIndex tileIndex, java.util.List<java.lang.Integer> requestedTiles, java.util.Set<IlluminaDataType> supportedTypes)
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.public void seekToTile(int oneBasedTileNumber)
public OUTPUT_RECORD next()
public boolean hasNext()
public int getTileOfNextCluster()
public void verifyData(java.util.List<java.lang.Integer> tiles, int[] cycles)
tiles
- The number of tiles in the current runcycles
- The number of cycles in the current runpublic java.util.Set<IlluminaDataType> supportedTypes()
public void remove()
public void close()