/** * Like {@link #fromBufferedStream(java.io.InputStream, LineReaderUtil.LineReaderOption)}, but the synchronicity * option is determined by {@link htsjdk.samtools.Defaults}: if asynchronous I/O is enabled, an asynchronous line reader will be * returned. */ public static LineReader fromBufferedStream(final InputStream stream) { return fromBufferedStream(stream, Defaults.USE_ASYNC_IO ? LineReaderOption.ASYNCHRONOUS : LineReaderOption.SYNCHRONOUS); }
@Override public LineIterator makeSourceFromStream(final InputStream bufferedInputStream) { return new LineIteratorImpl(LineReaderUtil.fromBufferedStream(bufferedInputStream)); }
public Iterator<T> iterator() { return this; } }
final LineIterator lineIterator = new LineIteratorImpl(LineReaderUtil.fromBufferedStream(bps, LineReaderUtil.LineReaderOption.SYNCHRONOUS)); final VCFCodec headerParser = new VCFCodec(); this.header = (VCFHeader) headerParser.readActualHeader(lineIterator);