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Fix vcf2zarr tests #1309

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Merged
merged 3 commits into from
Apr 14, 2025
Merged

Fix vcf2zarr tests #1309

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18138ca
Fix vcf2zarr tests
tomwhite Apr 14, 2025
3cae0f6
Update to schema format 0.5
tomwhite Apr 14, 2025
d4f06bf
Fix alleles dimension in GWAS tutorial schema
tomwhite Apr 14, 2025
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4 changes: 2 additions & 2 deletions sgkit/tests/io/test_vcf2zarr_compat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
import pytest

pytest.importorskip("bio2zarr")
from bio2zarr import vcf2zarr
from bio2zarr import icf
from bio2zarr.constants import (
FLOAT32_FILL,
FLOAT32_MISSING,
Expand All @@ -23,7 +23,7 @@ def test_vcf2zarr_compat(shared_datadir, tmp_path):
vcf_path = shared_datadir / "sample.vcf.gz"
vcz_path = tmp_path.joinpath("sample.vcz").as_posix()

vcf2zarr.convert(
icf.convert(
[vcf_path],
vcz_path,
variants_chunk_size=5,
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