/*
* 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 org.apache.log4j.Logger;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.variant.Variant;
import org.broad.igv.variant.vcf.VCFVariant;
import htsjdk.tribble.AsciiFeatureCodec;
import htsjdk.tribble.Feature;
import htsjdk.tribble.readers.LineIterator;
import htsjdk.variant.variantcontext.VariantContext;
import java.io.IOException;
/**
* @author Jim Robinson
* @date Aug 1, 2011
*/
public class VCFWrapperCodec extends AsciiFeatureCodec<VCFVariant> {
private static Logger log = Logger.getLogger(Variant.class);
AsciiFeatureCodec wrappedCodec;
Genome genome;
public VCFWrapperCodec(AsciiFeatureCodec wrappedCodec, Genome genome) {
super(VCFVariant.class);
this.wrappedCodec = wrappedCodec;
this.genome = genome;
}
@Override
public Feature decodeLoc(LineIterator iterator) throws IOException{
return wrappedCodec.decodeLoc(iterator);
}
@Override
public VCFVariant decode(String line) {
// VCFCodec supports completely missing fields (which would simply have a ".")
// but does not currently support missing only certain elements of a field.
// IGV is much more permissive.
VariantContext vc = null;
try {
vc = (VariantContext) wrappedCodec.decode(line);
//The genotype fields are loaded lazily, we force parsing here to
//catch the exception if necessary
if (vc != null) vc.getSampleNames();
} catch (NumberFormatException e) {
String msg = String.format("NumberFormatException on line: %s \n Attempting to reformat by replacing ,., with ,0,", line);
log.warn(msg);
String refLine = line.replaceAll(",\\.", ",0");
refLine = refLine.replaceAll("\\.,", "0,");
vc = (VariantContext) wrappedCodec.decode(refLine);
}
if (vc == null) {
return null;
}
String chr = genome == null ? vc.getChr() : genome.getChromosomeAlias(vc.getChr());
return new VCFVariant(vc, chr);
}
@Override
public Object readActualHeader(LineIterator reader) {
return wrappedCodec.readActualHeader(reader);
}
/**
* This function returns true iff the File potentialInput can be parsed by this
* codec.
* <p/>
* There is an assumption that there's never a situation where two different Codecs
* return true for the same file. If this occurs, the recommendation would be to error out.
* <p/>
* Note this function must never throw an error. All errors should be trapped
* and false returned.
*
* @param path the file to test for parsability with this codec
* @return true if potentialInput can be parsed, false otherwise
*/
@Override
public boolean canDecode(String path) {
return path.endsWith(".vcf") || path.endsWith(".vcf4") || path.endsWith(".vcf3");
}
}