def main(argv):
if len(argv) != 2:
print('Usage: {} <input_vcf>'.format(argv[0]))
sys.exit(-1)
in_vcf = argv[1]
total = 0
by_type = collections.defaultdict(int)
by_ref = collections.defaultdict(int)
with vcf.VcfReader(in_vcf) as reader:
for variant in reader:
total += 1
by_type[variant_utils.variant_type(variant)] += 1
by_ref[variant.reference_name] += 1
print('# variants: {}'.format(total))
print('# ref variants: {}'.format(by_type[variant_utils.VariantType.ref]))
print('# SNP variants: {}'.format(by_type[variant_utils.VariantType.snp]))
print('# indel variants: {}'.format(by_type[variant_utils.VariantType.indel]))
for k, v in sorted(by_ref.items()):
print('# variants in {}: {}'.format(k, v))
def test_variant_type(self, variant, expected): self.assertEqual(variant_utils.variant_type(variant), expected)
