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Updates for latest vcztools changes #50

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Merged
tomwhite merged 1 commit into from
Apr 23, 2026
Merged

Updates for latest vcztools changes #50

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6 changes: 3 additions & 3 deletions tests/test_remove.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ def test_remove(tmp_path):
# check equivalence with original VCF (with sample subsetting)
compare_vcf_and_vcz(
tmp_path,
"view --no-version -s NA00001,NA00003",
"view --no-version -s NA00001,NA00003 --no-update",
"sample.vcf.gz",
"view --no-version",
vcz,
Expand Down Expand Up @@ -55,7 +55,7 @@ def test_remove_multiple_chunks(tmp_path):
reduced_samples = ",".join(vcztools_out.strip().split("\n"))
compare_vcf_and_vcz(
tmp_path,
f"view --no-version -s {reduced_samples}",
f"view --no-version -s {reduced_samples} --no-update",
"chr22.vcf.gz",
"view --no-version",
vcz,
Expand Down Expand Up @@ -103,7 +103,7 @@ def test_remove_icechunk(tmp_path):
# check equivalence with original VCF (with sample subsetting)
compare_vcf_and_vcz(
tmp_path,
"view --no-version -s NA00001,NA00003",
"view --no-version -s NA00001,NA00003 --no-update",
"sample.vcf.gz",
"view --no-version --zarr-backend-storage icechunk",
vcz,
Expand Down
4 changes: 2 additions & 2 deletions uv.lock
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4 changes: 2 additions & 2 deletions vczstore/normalise.py
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Original file line number Diff line number Diff line change
Expand Up @@ -170,8 +170,8 @@ def index_variants(vcz1, vcz2, *, show_progress=False):
updated_allele_mappings = {}

fields = ["variant_contig", "variant_position", "variant_allele"]
it1 = VczReader(vcz1).variants(fields=fields)
it2 = peekable(VczReader(vcz2).variants(fields=fields))
it1 = VczReader(root1).variants(fields=fields)
it2 = peekable(VczReader(root2).variants(fields=fields))

with variants_progress(n_variants, "Index", show_progress) as pbar:
for i, variant in enumerate(it1):
Expand Down
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