/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
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.getCanonicalChrName(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);
}
}