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A Java API for high-throughput sequencing data (HTS) formats

There is a newer version: 4.3.0

package htsjdk.tribble;

import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.LocationAware;
import htsjdk.samtools.util.RuntimeIOException;
import htsjdk.tribble.index.tabix.TabixFormat;
import htsjdk.tribble.readers.PositionalBufferedStream;

import java.io.IOException;
import java.io.InputStream;

/**
 * Implements common methods of {@link FeatureCodec}s that read from {@link htsjdk.tribble.readers.PositionalBufferedStream}s.
 * @author mccowan
 */
abstract public class BinaryFeatureCodec implements FeatureCodec {
    @Override
    public PositionalBufferedStream makeSourceFromStream(final InputStream bufferedInputStream) {
        if (bufferedInputStream instanceof PositionalBufferedStream)
            return (PositionalBufferedStream) bufferedInputStream;
        else
            return new PositionalBufferedStream(bufferedInputStream);
    }

    /** {@link PositionalBufferedStream} is already {@link LocationAware}. */
    @Override
    public LocationAware makeIndexableSourceFromStream(final InputStream bufferedInputStream) {
        return makeSourceFromStream(bufferedInputStream);
    }

    @Override
    public void close(final PositionalBufferedStream source) {
        CloserUtil.close(source);
    }

    @Override
    public boolean isDone(final PositionalBufferedStream source) {
        try {
            return source.isDone();
        } catch (final IOException e) {
            throw new RuntimeIOException("Failure reading from stream.", e);
        }
    }

    /**
     * Marked as final because binary features could not be tabix indexed
     */
    @Override
    public final TabixFormat getTabixFormat() {
        throw new TribbleException("Binary codecs does not support tabix");
    }
}