Add test for GT in header, but not FORMAT

sgkit-dev · Jul 8, 2024 · 957fdd0 · 957fdd0
1 parent 399cdc6
commit 957fdd0
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Showing 4 changed files with 2 additions and 1 deletion.
diff --git a/bio2zarr/vcf2zarr/verification.py b/bio2zarr/vcf2zarr/verification.py
@@ -153,7 +153,7 @@ def verify(vcf_path, zarr_path, show_progress=False):
     chrom = root["contig_id"][:][root["variant_contig"][:]]
     vid = root["variant_id"][:]
     call_genotype = None
-    if "call_genotype" in root:
+    if "call_genotype" in root and root["call_genotype"].size > 0:
         call_genotype = iter(root["call_genotype"])
 
     vcf = cyvcf2.VCF(vcf_path)

diff --git a/tests/data/vcf/sample_no_genotypes_with_gt_header.vcf.gz b/tests/data/vcf/sample_no_genotypes_with_gt_header.vcf.gz
diff --git a/tests/data/vcf/sample_no_genotypes_with_gt_header.vcf.gz.csi b/tests/data/vcf/sample_no_genotypes_with_gt_header.vcf.gz.csi
diff --git a/tests/test_vcf_examples.py b/tests/test_vcf_examples.py
@@ -834,6 +834,7 @@ def test_duplicate_paths(self, tmp_path):
         "sample.vcf.gz",
         "sample_old_tabix.vcf.gz",
         "sample_no_genotypes.vcf.gz",
+        "sample_no_genotypes_with_gt_header.vcf.gz",
         "1kg_2020_chrM.vcf.gz",
         "field_type_combos.vcf.gz",
         "out_of_order_contigs.vcf.gz",