Class MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>

  • 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 Detail

      • 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 Detail

      • seekToTile

        public void seekToTile​(int oneBasedTileNumber)
      • 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)
      • remove

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

        public abstract void close()