public static Pair<VCFHeader, List<VariantContext>> readVCF(final File source) throws IOException {
// read in the features
final List<VariantContext> vcs = new ArrayList<VariantContext>();
final VCFCodec codec = new VCFCodec();
PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source));
final LineIterator vcfSource = codec.makeSourceFromStream(pbs);
try {
final VCFHeader vcfHeader = (VCFHeader) codec.readActualHeader(vcfSource);
while (vcfSource.hasNext()) {
final VariantContext vc = codec.decode(vcfSource);
if ( vc != null )
vcs.add(vc);
}