def test_infer_mismatched_info_field_no_mismatches(self):
variant = self._get_sample_variant_info_ia_float_2_0_in_list()
infos = {
'IS': createInfo('IS', 1, 'String', ''),
'ISI': createInfo('ISI', 1, 'Integer', ''),
'ISF': createInfo('ISF', 1, 'Float', ''),
'IF': createInfo('IF', 1, 'Float', ''),
'IB': createInfo('IB', 0, 'Flag', ''),
'IA': createInfo('IA', 'A', 'Integer', '')
}
corrected_info = infer_headers_util._infer_mismatched_info_field(
'IA', variant.info.get('IA'),
vcf_header_io.VcfHeader(infos=infos).infos.get('IA'),
len(variant.alternate_bases))
self.assertEqual(None, corrected_info)
def test_infer_mismatched_info_field_correct_type(self):
variant = self._get_sample_variant_info_ia_cardinality_mismatch()
infos = {
'IS': createInfo('IS', 1, 'String', ''),
'ISI': createInfo('ISI', 1, 'Integer', ''),
'ISF': createInfo('ISF', 1, 'Float', ''),
'IF': createInfo('IF', 1, 'Float', ''),
'IB': createInfo('IB', 0, 'Flag', ''),
'IA': createInfo('IA', '.', 'Integer', '')
}
corrected_info = infer_headers_util._infer_mismatched_info_field(
'IA', variant.info.get('IA'),
vcf_header_io.VcfHeader(infos=infos).infos.get('IA'),
len(variant.alternate_bases))
expected = createInfo('IA', '.', 'Float', '')
self.assertEqual(expected, corrected_info)