Class AbstractIlluminaPositionFileReader

java.lang.Object
picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
All Implemented Interfaces:
htsjdk.samtools.util.CloseableIterator<AbstractIlluminaPositionFileReader.PositionInfo>, Closeable, AutoCloseable, Iterator<AbstractIlluminaPositionFileReader.PositionInfo>
Direct Known Subclasses:
ClocsFileReader, LocsFileReader, PosFileReader

public abstract class AbstractIlluminaPositionFileReader extends Object implements htsjdk.samtools.util.CloseableIterator<AbstractIlluminaPositionFileReader.PositionInfo>
The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs. Each of these file types we read sequentially and are really concerned with iterating over the coordinates and returning them as as they would appear in a QSeq file. Therefore, this abstract base class provides the basic functionality for iterating over the values found in these files and converting them into qseq style coordinates.

Currently these readers also return lane/tile but this will be unnecessary in future releases.

  • Field Details

    • MAX_POS

      public static final float MAX_POS
      See Also:
    • MIN_POS

      public static final float MIN_POS
      At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small negative values and see what happens.
      See Also:
    • S_LOCS_FILE

      public static final String S_LOCS_FILE
      See Also:
  • Constructor Details

    • AbstractIlluminaPositionFileReader

      public AbstractIlluminaPositionFileReader(File file)
    • AbstractIlluminaPositionFileReader

      public AbstractIlluminaPositionFileReader(File file, int lane, int tile)
      Use this ctor if lane and tile are not discernible from file name.
      Parameters:
      file - The position file to read.
      lane - The lane to read positions for.
      tile - The tile to read positions for.
  • Method Details