boolean isVCF = codec.getClass().isAssignableFrom(VCFCodec.class);
TestUtils.createIndex(vcfFile);
AbstractFeatureReader basicReader = AbstractFeatureReader.getFeatureReader(vcfFile, codec, true);
CloseableTribbleIterator it = basicReader.iterator();
List<VCFVariant> features = new ArrayList<VCFVariant>();
while (it.hasNext()) {
VCFVariant next = (VCFVariant) it.next();
features.add(next);
}
// Test the first feature in the file -- this one was failing
VCFVariant a_6321732 = (VCFVariant) FeatureUtils.getFeatureClosest(6321732.4, features);
assertEquals("variant closest to 6321732 must be found with position=6321732", 6321732, a_6321732.getStart());