def grch38_vep95_annotated_variants_info_fixed(test_root: Path) -> List[Variant]:
return list(
Variant.read_and_parse_vcf(
test_root.joinpath("examples/grch38_vep95_50_variants.info_fixed.vcf.gz")
)
)
def test_read_vcf_detect_vep_version(
test_root: Path, caplog, vcf_pth: Path, vep_ver: int
):
reader = Variant.read_and_parse_vcf(test_root.joinpath(vcf_pth))
next(reader)
assert f"VEP version {vep_ver}" in caplog.text
def grch37_vep85_annotated_variants(test_root: Path):
return list(
Variant.read_and_parse_vcf(
test_root / "examples" / "grch37_vep85_5_variants.vcf"
)
)
def charger_result(test_root: Path):
variant = next(
Variant.read_and_parse_vcf(test_root / "examples" /
"grch37_vep85_5_variants.vcf"))
return CharGerResult(variant)