do alleles field validation only if it exists on ht

Author: jklugherz

v03_pipeline/lib/misc/validation.py

@@ -31,6 +31,9 @@ def validate_allele_type(
     **_: Any,
 ) -> None:
     ht = t.rows() if isinstance(t, hl.MatrixTable) else t
+    if not hasattr(ht, 'alleles'):
+        return
+
     ht = ht.filter(
         dataset_type.invalid_allele_types.contains(
             hl.numeric_allele_type(ht.alleles[0], ht.alleles[1]),

v03_pipeline/lib/reference_datasets/gnomad_svs_test.py

@@ -0,0 +1,63 @@
+import unittest
+from unittest.mock import patch
+
+import hail as hl
+
+from v03_pipeline.lib.model import ReferenceGenome
+from v03_pipeline.lib.reference_datasets.reference_dataset import ReferenceDataset
+
+TEST_GNOMAD_SVS_RAW_HT = (
+    'v03_pipeline/var/test/reference_datasets/raw/gnomad_svs_from_vcf.ht'
+)
+
+
+class GnomadSVsTest(unittest.TestCase):
+    @patch('v03_pipeline.lib.reference_datasets.gnomad_svs.vcf_to_ht')
+    def test_gnomad_svs(self, mock_vcf_to_ht):
+        mock_vcf_to_ht.return_value = hl.read_table(TEST_GNOMAD_SVS_RAW_HT)
+        ht = ReferenceDataset.gnomad_svs.get_ht(ReferenceGenome.GRCh38)
+        self.assertEqual(
+            ht.collect(),
+            [
+                hl.Struct(
+                    KEY='gnomAD-SV_v3_BND_chr1_1a45f73a',
+                    AF=0.11413399875164032,
+                    AC=8474,
+                    AN=74246,
+                    N_HET=8426,
+                    N_HOMREF=28673,
+                ),
+                hl.Struct(
+                    KEY='gnomAD-SV_v3_BND_chr1_3fa36917',
+                    AF=0.004201000090688467,
+                    AC=466,
+                    AN=110936,
+                    N_HET=466,
+                    N_HOMREF=55002,
+                ),
+                hl.Struct(
+                    KEY='gnomAD-SV_v3_BND_chr1_7bbf34b5',
+                    AF=0.03698499873280525,
+                    AC=3119,
+                    AN=84332,
+                    N_HET=3115,
+                    N_HOMREF=39049,
+                ),
+                hl.Struct(
+                    KEY='gnomAD-SV_v3_BND_chr1_933a2971',
+                    AF=0.3238990008831024,
+                    AC=21766,
+                    AN=67200,
+                    N_HET=21616,
+                    N_HOMREF=11909,
+                ),
+                hl.Struct(
+                    KEY='gnomAD-SV_v3_DUP_chr1_01c2781c',
+                    AF=0.0019970000721514225,
+                    AC=139,
+                    AN=69594,
+                    N_HET=139,
+                    N_HOMREF=34658,
+                ),
+            ],
+        )

v03_pipeline/var/test/reference_datasets/raw/gnomad_svs_from_vcf.ht/.README.txt.crc

@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.133-4c60fddb171a
+  Created at 2025/03/04 14:19:46