/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.feature.tribble;
import htsjdk.samtools.util.LocationAware;
import org.apache.log4j.Logger;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.variant.vcf.VCFVariant;
import htsjdk.tribble.Feature;
import htsjdk.tribble.FeatureCodec;
import htsjdk.tribble.FeatureCodecHeader;
import htsjdk.tribble.readers.AsciiLineReader;
import htsjdk.tribble.readers.AsciiLineReaderIterator;
import htsjdk.tribble.readers.PositionalBufferedStream;
import htsjdk.variant.variantcontext.VariantContext;
import java.io.IOException;
import java.io.InputStream;
/**
* @author Jacob Silterra
* @date 2013-Jun-14
*/
public class BCF2WrapperCodec implements FeatureCodec<VCFVariant, PositionalBufferedStream> {
private static Logger log = Logger.getLogger(BCF2WrapperCodec.class);
FeatureCodec<VariantContext, PositionalBufferedStream> wrappedCodec;
Genome genome;
public BCF2WrapperCodec(FeatureCodec<VariantContext, PositionalBufferedStream> wrappedCodec, Genome genome) {
this.wrappedCodec = wrappedCodec;
this.genome = genome;
}
@Override
public VCFVariant decode(PositionalBufferedStream stream) throws IOException {
VariantContext vc = wrappedCodec.decode(stream);
if (vc == null) {
return null;
}
String chr = genome == null ? vc.getChr() : genome.getChromosomeAlias(vc.getChr());
return new VCFVariant(vc, chr);
}
@Override
public Feature decodeLoc(PositionalBufferedStream stream) throws IOException {
return this.wrappedCodec.decodeLoc(stream);
}
@Override
public FeatureCodecHeader readHeader(PositionalBufferedStream stream) throws IOException {
return this.wrappedCodec.readHeader(stream);
}
@Override
public Class<VCFVariant> getFeatureType() {
return VCFVariant.class;
}
@Override
public boolean canDecode(String path) {
return path.endsWith(".bcf");
}
@Override
public LocationAware makeIndexableSourceFromStream(final InputStream bufferedInputStream) {
final PositionalBufferedStream pbs;
if (bufferedInputStream instanceof PositionalBufferedStream) {
pbs = (PositionalBufferedStream) bufferedInputStream;
} else {
pbs = new PositionalBufferedStream(bufferedInputStream);
}
return new AsciiLineReaderIterator(new AsciiLineReader(pbs));
}
@Override
public boolean isDone(PositionalBufferedStream positionalBufferedStream) {
try {
return positionalBufferedStream.isDone();
} catch (IOException e) {
log.error(e.getMessage(), e);
return true;
}
}
@Override
public void close(PositionalBufferedStream positionalBufferedStream) {
positionalBufferedStream.close();
}
@Override
public PositionalBufferedStream makeSourceFromStream(final InputStream bufferedInputStream) {
return new PositionalBufferedStream(bufferedInputStream);
}
}