/**
* Utility class to read all of the VC records from a file
*
* @param file
* @param codec
* @return
* @throws java.io.IOException
*/
public static final <SOURCE> Pair<VCFHeader, VCIterable<SOURCE>> readAllVCs(
final File file, final FeatureCodec<VariantContext, SOURCE> codec) throws IOException {
// read in the features
SOURCE source = codec.makeSourceFromStream(new FileInputStream(file));
FeatureCodecHeader header = codec.readHeader(source);
final VCFHeader vcfHeader = (VCFHeader) header.getHeaderValue();
return new Pair<>(vcfHeader, new VCIterable<>(source, codec, vcfHeader));
}
@Override
public VariantContext next() {
try {
final VariantContext vc = codec.decode(nextSource());
return vc == null ? null : vc.fullyDecode(header, false);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
@Override
public boolean hasNext() {
return !codec.isDone(source);
}