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Add contig_lengths dataset attribute if found in the VCF file #946

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merged 2 commits into from
Nov 3, 2022
Merged

Add contig_lengths dataset attribute if found in the VCF file #946

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94fbd4e
Add `contig_lengths` dataset attribute if found in the VCF file
tomwhite Nov 2, 2022
eedb175
Fix scikit-allel roundtrip test when contig lengths found
tomwhite Nov 2, 2022
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4 changes: 4 additions & 0 deletions sgkit/io/vcf/vcf_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -525,6 +525,10 @@ def vcf_to_zarr_sequential(
ds.attrs["filters"] = filters
ds.attrs["vcf_zarr_version"] = "0.1"
ds.attrs["vcf_header"] = vcf.raw_header
try:
ds.attrs["contig_lengths"] = vcf.seqlens
except AttributeError:
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Checking the cyvcf2 source I see that this raises if the lengths are absent in the header, so seem ok to then omit them in our output.

pass

for field_handler in field_handlers:
field_handler.update_dataset(ds)
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3 changes: 3 additions & 0 deletions sgkit/tests/io/vcf/test_vcf_reader.py
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Expand Up @@ -32,6 +32,7 @@ def test_vcf_to_zarr__small_vcf(shared_datadir, is_path, tmp_path):
ds = xr.open_zarr(output)

assert ds.attrs["contigs"] == ["19", "20", "X"]
assert "contig_lengths" not in ds.attrs
assert_array_equal(ds["variant_contig"], [0, 0, 1, 1, 1, 1, 1, 1, 2])
assert_array_equal(
ds["variant_position"],
Expand Down Expand Up @@ -155,6 +156,8 @@ def test_vcf_to_zarr__large_vcf(shared_datadir, is_path, tmp_path):
vcf_to_zarr(path, output, chunk_length=5_000)
ds = xr.open_zarr(output)

assert ds.attrs["contigs"] == ["20", "21"]
assert ds.attrs["contig_lengths"] == [63025520, 48129895]
assert ds["sample_id"].shape == (1,)
assert ds["call_genotype"].shape == (19910, 1, 2)
assert ds["call_genotype_mask"].shape == (19910, 1, 2)
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3 changes: 3 additions & 0 deletions sgkit/tests/io/vcf/test_vcf_roundtrip.py
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Expand Up @@ -199,6 +199,9 @@ def test_all_fields(
assert allel_ds_contigs <= sg_ds_contigs
del allel_ds.attrs["contigs"]
del sg_ds.attrs["contigs"]
# scikit-allel doesn't store contig lengths
if "contig_lengths" in sg_ds.attrs:
del sg_ds.attrs["contig_lengths"]

if allel_ds_contigs < sg_ds_contigs:
# variant_contig variables are not comparable, so remove them before comparison
Expand Down