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.
  • Constructor Details

    • 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.
  • Method Details

    • seekToTile

      public void seekToTile(int oneBasedTileNumber)
    • next

      public OUTPUT_RECORD next()
      Specified by:
      next in interface Iterator<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
    • hasNext

      public boolean hasNext()
      Specified by:
      hasNext in interface Iterator<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
    • getTileOfNextCluster

      public int getTileOfNextCluster()
    • verifyData

      public void verifyData(List<Integer> tiles, int[] cycles)
    • supportedTypes

      public Set<IlluminaDataType> supportedTypes()
    • remove

      public void remove()
      Specified by:
      remove in interface Iterator<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
    • close

      void close()