diff --git a/tests/test_stats.py b/tests/test_stats.py index 7a28c3f..9f1b9c3 100644 --- a/tests/test_stats.py +++ b/tests/test_stats.py @@ -3,7 +3,7 @@ import pytest import zarr -from bio2zarr import vcf2zarr +from bio2zarr import vcf from vcztools.stats import nrecords, stats @@ -39,7 +39,7 @@ def test_stats__no_index(tmp_path): original = pathlib.Path("tests/data/vcf") / "sample.vcf.gz" # don't use cache here since we want to make sure vcz is not indexed vcz = tmp_path.joinpath("intermediate.vcz") - vcf2zarr.convert([original], vcz, worker_processes=0, local_alleles=False) + vcf.convert([original], vcz, worker_processes=0, local_alleles=False) # delete the index created by vcf2zarr root = zarr.open(vcz, mode="a") diff --git a/tests/test_vcf_writer.py b/tests/test_vcf_writer.py index 6ec9619..a00f5e9 100644 --- a/tests/test_vcf_writer.py +++ b/tests/test_vcf_writer.py @@ -6,7 +6,7 @@ import numpy as np import pytest import zarr -from bio2zarr import vcf2zarr +from bio2zarr import vcf from cyvcf2 import VCF from numpy.testing import assert_array_equal @@ -305,7 +305,7 @@ def test_write_vcf__generate_header(tmp_path): original = pathlib.Path("tests/data/vcf") / "sample.vcf.gz" # don't use cache here since we mutate the vcz vcz = tmp_path.joinpath("intermediate.vcz") - vcf2zarr.convert([original], vcz, worker_processes=0, local_alleles=False) + vcf.convert([original], vcz, worker_processes=0, local_alleles=False) # remove vcf_header root = zarr.open(vcz, mode="r+") diff --git a/tests/utils.py b/tests/utils.py index 6eb5c29..f7fda49 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -5,7 +5,7 @@ import cyvcf2 import numpy as np -from bio2zarr import vcf2zarr +from bio2zarr import vcf @contextmanager @@ -145,7 +145,7 @@ def vcz_path_cache(vcf_path): cached_vcz_path = (cache_path / vcf_path.name).with_suffix(".vcz") if not cached_vcz_path.exists(): if vcf_path.name.startswith("chr22"): - vcf2zarr.convert( + vcf.convert( [vcf_path], cached_vcz_path, worker_processes=0, @@ -153,7 +153,7 @@ def vcz_path_cache(vcf_path): samples_chunk_size=10, ) else: - vcf2zarr.convert( + vcf.convert( [vcf_path], cached_vcz_path, worker_processes=0, local_alleles=False ) return cached_vcz_path