Examples of FilterFileReader

picard.illumina.parser.readers.FilterFileReader
Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not. These values are written as sequential bytes to Filter Files. The structure of a filter file is as follows: Bytes 0-3 : 0 Bytes 4-7 : unsigned int version Bytes 8-11 : unsigned int numClusters

Examples of picard.illumina.parser.readers.FilterFileReader


    /** Wrap a filterFile reader in a closeable iterator and return it*/
    @Override
    protected CloseableIterator<PfData> makeTileIterator(final File iterator) {
        return new CloseableIterator<PfData>() {
            private FilterFileReader reader = new FilterFileReader(iterator);


            public void close() {
                reader = null;
            }


            public boolean hasNext() {
                return reader.hasNext();
            }


            public PfData next() {
                final boolean nextValue = reader.next();
                return new PfData() {
                    public boolean isPf() {
                        return nextValue;
                    }
                };

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Examples of picard.illumina.parser.readers.FilterFileReader

public class MultiTileFilterParser extends MultiTileParser<PfData> {
    private final FilterFileReader reader;


    public MultiTileFilterParser(final TileIndex tileIndex, final List<Integer> requestedTiles, final File filterFile) {
        super(tileIndex, requestedTiles, Collections.singleton(IlluminaDataType.PF));
        reader = new FilterFileReader(filterFile);
    }

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