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.
  • Constructor Details

    • PerTileParser

      public PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles)
    • PerTileParser

      public PerTileParser(picard.illumina.parser.IlluminaFileMap tilesToFiles, int nextTile)
  • Method Details

    • 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
    • seekToTile

      public void seekToTile(int oneBasedTileNumber)
    • maybeAdvance

      public void maybeAdvance()
    • next

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

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

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

      public void close()
    • verifyData

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

      Set<IlluminaDataType> supportedTypes()
      The DataTypes that this parser can provide