def test_main(self):
in_fname = test_utils.genomics_core_testdata('test_allele_depth.vcf')
out_fname = test_utils.test_tmpfile('output.vcf')
add_ad_to_vcf.main(['add_ad_to_vcf', in_fname, out_fname])
with vcf.VcfReader(out_fname, use_index=False) as reader:
info_ids = [info.id for info in reader.header.infos]
self.assertTrue('AD' in info_ids)
variant1 = next(reader)
self.assertEqual([3, 3], variant_utils.get_info(variant1, 'AD', reader))
variant2 = next(reader)
self.assertEqual([30, 44], variant_utils.get_info(variant2, 'AD', reader))
variant3 = next(reader)
self.assertEqual([15, 4], variant_utils.get_info(variant3, 'AD', reader))
variant4 = next(reader)
self.assertEqual([2, 4], variant_utils.get_info(variant4, 'AD', reader))
variant5 = next(reader)
self.assertEqual([24, 2], variant_utils.get_info(variant5, 'AD', reader))
def test_get_info(self, field_name, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.info_field_get_fn.return_value = (
functools.partial(
struct_utils.get_string_field, is_single_field=True))
variant = variants_pb2.Variant()
variant_utils.set_info(variant, 'AD', [23, 25])
variant_utils.set_info(variant, 'AA', 'C')
variant_utils.set_info(variant, '1000G', True)
variant_utils.set_info(variant, 'DB', False)
actual = variant_utils.get_info(variant, field_name, vcf_object=reader)
self.assertEqual(actual, expected)