@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);
}
}
private static void makeEmpiricalTests() throws IOException {
if (ENABLE_SOURCE_VCF_TESTS) {
for (final File file : testSourceVCFs) {
VCFCodec codec = new VCFCodec();
VariantContextContainer x = readAllVCs(file, codec);
List<VariantContext> fullyDecoded = new ArrayList<VariantContext>();
for (final VariantContext raw : x.getVCs()) {
if (raw != null) fullyDecoded.add(raw.fullyDecode(x.getHeader(), false));
}
TEST_DATAs.add(new VariantContextTestData(x.getHeader(), fullyDecoded));
}
}
}
