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Merged
tomwhite merged 3 commits into from
Apr 20, 2026
Merged

Add normalise test using VCF data #47

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a145d72
Fix case of no compression
tomwhite Apr 20, 2026
b6d2ee2
Add normalise test using VCF data
tomwhite Apr 20, 2026
d73d3f2
Update bio2zarr
tomwhite Apr 20, 2026
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18 changes: 18 additions & 0 deletions tests/test_normalise.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,16 @@
import zarr
from numpy.testing import assert_array_equal

from vczstore.append import append
from vczstore.normalise import (
index_variants,
normalise,
remap_genotypes,
variant_alleles_are_equivalent,
)

from .utils import compare_vcf_and_vcz, convert_vcf_to_vcz


# TODO: replace this with make_vcz in vcztools/bio2zarr
# see https://github.com/sgkit-dev/vczstore/issues/37
Expand Down Expand Up @@ -324,3 +327,18 @@ def test_normalise__other_call_fields_not_implemented():

with pytest.raises(NotImplementedError):
normalise(vcz1, vcz2, vcz2_norm)


def test_normalise_and_append(tmp_path):
vcz0 = convert_vcf_to_vcz("sample-variants.vcf.gz", tmp_path, ploidy=2)
vcz1 = convert_vcf_to_vcz("sample-part1.vcf.gz", tmp_path)
vcz1_norm = zarr.storage.MemoryStore()

normalise(vcz0, vcz1, vcz1_norm)

append(vcz0, vcz1_norm)

# check equivalence with original VCF
compare_vcf_and_vcz(
tmp_path, "view --no-version", "sample-part1.vcf.gz", "view --no-version", vcz0
)
4 changes: 2 additions & 2 deletions uv.lock
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6 changes: 3 additions & 3 deletions vczstore/normalise.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import numpy as np
import zarr
from bio2zarr.zarr_utils import create_empty_group_array, get_compressor
from bio2zarr.zarr_utils import create_empty_group_array, get_compressor_config
from more_itertools import peekable
from vcztools.constants import STR_FILL, STR_MISSING
from vcztools.retrieval import VczReader
Expand Down Expand Up @@ -51,7 +51,7 @@ def normalise(vcz1, vcz2, vcz2_norm):
shape=shape,
dtype=arr.dtype,
chunks=chunks,
compressor=get_compressor(arr),
compressor=get_compressor_config(arr),
dimension_names=array_dims(arr),
)
else:
Expand All @@ -66,7 +66,7 @@ def normalise(vcz1, vcz2, vcz2_norm):
shape=arr.shape,
dtype=arr.dtype,
chunks=arr.chunks,
compressor=get_compressor(arr),
compressor=get_compressor_config(arr),
dimension_names=array_dims(arr),
)

Expand Down
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