def main(argv):
if len(argv) != 3:
print('Usage: %s <input_vcf> <output_vcf>' % argv[0])
sys.exit(-1)
in_vcf = argv[1]
out_vcf = argv[2]
with vcf.VcfReader(in_vcf) as reader:
if 'AD' in [info.id for info in reader.header.infos]:
print('%s already contains AD field.' % in_vcf)
sys.exit(-1)
out_header = reader.header
out_header.infos.extend([vcf_constants.reserved_info_field('AD')])
with vcf.VcfWriter(out_vcf, header=out_header) as writer:
for variant in reader:
variant_utils.set_info(variant, 'AD', get_variant_ad(variant),
writer)
writer.write(variant)
def test_invalid_get_reserved_info(self, field_id):
with self.assertRaisesRegexp(ValueError, 'No reserved field with id'):
vcf_constants.reserved_info_field(field_id)
def test_get_reserved_info(self, field_id):
info = vcf_constants.reserved_info_field(field_id)
self.assertIsInstance(info, variants_pb2.VcfInfo)
self.assertEqual(info.id, field_id)