def test_partition_into_regions__missing_index(shared_datadir, is_path):
vcf_path = path_for_test(shared_datadir,
"CEUTrio.20.21.gatk3.4.noindex.g.vcf.bgz",
is_path)
with pytest.raises(ValueError, match=r"Cannot find .tbi or .csi file."):
partition_into_regions(vcf_path, num_parts=2)
bogus_index_path = path_for_test(
shared_datadir, "CEUTrio.20.21.gatk3.4.noindex.g.vcf.bgz.index",
is_path)
with pytest.raises(ValueError,
match=r"Only .tbi or .csi indexes are supported."):
partition_into_regions(vcf_path,
index_path=bogus_index_path,
num_parts=2)
def test_partition_into_regions__num_parts(shared_datadir, vcf_file, is_path):
vcf_path = path_for_test(shared_datadir, vcf_file, is_path)
regions = partition_into_regions(vcf_path, num_parts=4)
assert regions is not None
part_variant_counts = [
count_variants(vcf_path, region) for region in regions
]
total_variants = count_variants(vcf_path)
assert sum(part_variant_counts) == total_variants
def test_partition_into_regions__target_part_size(shared_datadir, is_path):
vcf_path = path_for_test(shared_datadir, "CEUTrio.20.21.gatk3.4.g.vcf.bgz",
is_path)
regions = partition_into_regions(vcf_path, target_part_size=100_000)
assert regions is not None
assert len(regions) == 5
part_variant_counts = [
count_variants(vcf_path, region) for region in regions
]
total_variants = count_variants(vcf_path)
assert sum(part_variant_counts) == total_variants
def test_partition_into_regions__invalid_arguments(shared_datadir, is_path):
vcf_path = path_for_test(shared_datadir, "CEUTrio.20.21.gatk3.4.g.vcf.bgz",
is_path)
with pytest.raises(
ValueError,
match=r"One of num_parts or target_part_size must be specified"):
partition_into_regions(vcf_path)
with pytest.raises(
ValueError,
match=r"Only one of num_parts or target_part_size may be specified"
):
partition_into_regions(vcf_path, num_parts=4, target_part_size=100_000)
with pytest.raises(ValueError, match=r"num_parts must be positive"):
partition_into_regions(vcf_path, num_parts=0)
with pytest.raises(ValueError, match=r"target_part_size must be positive"):
partition_into_regions(vcf_path, target_part_size=0)
def test_partition_into_regions__one_part(shared_datadir, is_path):
vcf_path = path_for_test(shared_datadir, "CEUTrio.20.21.gatk3.4.g.vcf.bgz",
is_path)
assert partition_into_regions(vcf_path, num_parts=1) is None