Check dimension sizes for named VCF Number fields

Author: tomwhite

bio2zarr/icf.py

@@ -1054,11 +1054,15 @@ def generate_schema(
             f"{schema_instance.variants_chunk_size, schema_instance.samples_chunk_size}"
         )
 
+        alt_field = self.fields["ALT"]
+        max_alleles = alt_field.vcf_field.summary.max_number + 1
+
         def spec_from_field(field, array_name=None):
             return vcz.ZarrArraySpec.from_field(
                 field,
                 num_samples=n,
                 num_variants=m,
+                max_alleles=max_alleles,
                 samples_chunk_size=schema_instance.samples_chunk_size,
                 variants_chunk_size=schema_instance.variants_chunk_size,
                 array_name=array_name,
@@ -1088,9 +1092,6 @@ def fixed_field_spec(
                 compressor=compressor,
             )
 
-        alt_field = self.fields["ALT"]
-        max_alleles = alt_field.vcf_field.summary.max_number + 1
-
         array_specs = [
             fixed_field_spec(
                 name="variant_contig",

bio2zarr/vcz.py

@@ -119,6 +119,7 @@ def from_field(
         *,
         num_variants,
         num_samples,
+        max_alleles,
         variants_chunk_size,
         samples_chunk_size,
         array_name=None,
@@ -137,23 +138,38 @@ def from_field(
         if array_name is None:
             array_name = prefix + vcf_field.name
 
-        # TODO make an option to add in the empty extra dimension
         max_number = vcf_field.max_number
-        if (max_number > 0 and vcf_field.vcf_number in ("R", "A", "G")) or (
-            max_number > 1 or vcf_field.full_name == "FORMAT/LAA"
-        ):
-            shape.append(max_number)
-            chunks.append(max_number)
-            # TODO we should really be checking this to see if the named dimensions
-            # are actually correct.
-            if vcf_field.vcf_number == "R":
+        if vcf_field.vcf_number == "R":
+            if max_number > max_alleles:
+                raise ValueError(
+                    f"Max number of values {max_number} exceeds max alleles "
+                    f"{max_alleles} for {vcf_field.full_name}"
+                )
+            if max_alleles > 0:
+                shape.append(max_alleles)
+                chunks.append(max_alleles)
                 dimensions.append("alleles")
-            elif vcf_field.vcf_number == "A":
+        elif vcf_field.vcf_number == "A":
+            max_alt_alleles = max_alleles - 1
+            if max_number > max_alt_alleles:
+                raise ValueError(
+                    f"Max number of values {max_number} exceeds max alt alleles "
+                    f"{max_alt_alleles} for {vcf_field.full_name}"
+                )
+            if max_alt_alleles > 0:
+                shape.append(max_alt_alleles)
+                chunks.append(max_alt_alleles)
                 dimensions.append("alt_alleles")
-            elif vcf_field.vcf_number == "G":
-                dimensions.append("genotypes")
-            else:
-                dimensions.append(f"{vcf_field.category}_{vcf_field.name}_dim")
+        elif max_number > 0 and vcf_field.vcf_number == "G":
+            # TODO: need max_genotypes
+            shape.append(max_number)
+            chunks.append(max_number)
+            dimensions.append("genotypes")
+        elif max_number > 1 or vcf_field.full_name == "FORMAT/LAA":
+            # TODO make an option to add in the empty extra dimension
+            shape.append(max_number)
+            chunks.append(max_number)
+            dimensions.append(f"{vcf_field.category}_{vcf_field.name}_dim")
         return ZarrArraySpec(
             source=vcf_field.full_name,
             name=array_name,