Ensure gnomad sv missing migration (#1085)

Author: bpblanken

Diff for: v03_pipeline/migrations/annotations/0006_ensure_gnomad_sv_missing.py

@@ -0,0 +1,21 @@
+import hail as hl
+
+from v03_pipeline.lib.migration.base_migration import BaseMigration
+from v03_pipeline.lib.model import DatasetType, ReferenceGenome
+
+
+class EnsureGnomadSVMissing(BaseMigration):
+    reference_genome_dataset_types: frozenset[tuple[ReferenceGenome, DatasetType]] = (
+        frozenset(
+            ((ReferenceGenome.GRCh38, DatasetType.SV),),
+        )
+    )
+
+    @staticmethod
+    def migrate(ht: hl.Table, **_) -> hl.Table:
+        return ht.annotate(
+            gnomad_svs=hl.or_missing(
+                hl.any([hl.is_defined(x) for x in ht.gnomad_svs.values()]),
+                ht.gnomad_svs,
+            ),
+        )