Examples of picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

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.

     * @return An iterator over the PositionalData in that file.
     */
    @Override
    protected CloseableIterator<PositionalData> makeTileIterator(final File file) {


        final AbstractIlluminaPositionFileReader fileReader;
        switch(fileType){
            case Pos:
                fileReader = new PosFileReader(file);
                break;

Related Classes of picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

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