Package picard.illumina.parser

Class PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>

  • 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 Detail

      • PerTileParser

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

      • PerTileParser

        public PerTileParser​(picard.illumina.parser.IlluminaFileMap tilesToFiles,
                     int nextTile)

    • Method Detail

      • 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()

      • 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

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