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Fix bio2zarr import #218

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Fix bio2zarr import #218

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4 changes: 2 additions & 2 deletions tests/test_stats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

import pytest
import zarr
from bio2zarr import vcf2zarr
from bio2zarr import vcf

from vcztools.stats import nrecords, stats

Expand Down Expand Up @@ -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")
Expand Down
4 changes: 2 additions & 2 deletions tests/test_vcf_writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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+")
Expand Down
6 changes: 3 additions & 3 deletions tests/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

import cyvcf2
import numpy as np
from bio2zarr import vcf2zarr
from bio2zarr import vcf


@contextmanager
Expand Down Expand Up @@ -145,15 +145,15 @@ 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,
variants_chunk_size=10,
samples_chunk_size=10,
)
else:
vcf2zarr.convert(
vcf.convert(
[vcf_path], cached_vcz_path, worker_processes=0, local_alleles=False
)
return cached_vcz_path
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