Set h4/r2 to NULL for orphans

Also allow single signals with NULLs for those values to still come through regardless of filter value

Author: welchr

colocus/api/filters.py

@@ -26,6 +26,19 @@ def parse_region(region):
         return match.groups()
 
 
+class NumberFilterWithNulls(NumberFilter):
+    """NumberFilter that includes NULL values when filtering."""
+
+    def filter(self, qs, value):
+        if value is None:
+            return qs
+
+        lookup = f"{self.field_name}__{self.lookup_expr}"
+        return qs.filter(
+            Q(**{lookup: value}) | Q(**{f"{self.field_name}__isnull": True})
+        )
+
+
 class NullsLastOrderingFilter(OrderingFilter):
     """OrderingFilter that always puts NULL values last."""
 
@@ -432,10 +445,10 @@ def filter_signal2_trait(self, queryset, name, value):
         label="Minimum -log10 p-value for signal 2",
     )
 
-    min_h4 = NumberFilter(
+    min_h4 = NumberFilterWithNulls(
         field_name="coloc_h4", lookup_expr="gte", label="Minimum PP(H4)"
     )
-    min_r2 = NumberFilter(
+    min_r2 = NumberFilterWithNulls(
         field_name="r2",
         lookup_expr="gte",
         label="Minimum r2 between the two signals' lead variants",

colocus/core/migrations/0006_colocresult_with_orphans.py

@@ -42,10 +42,10 @@ class Migration(migrations.Migration):
   SELECT
     fs.uuid as uuid,
     NULL::jsonb as cross_signal,
-    0.0::float8 as coloc_h3,
-    0.0::float8 as coloc_h4,
-    0.0::float8 as r2,
-    0::integer as n_coloc_between_traits,
+    NULL::float8 as coloc_h3,
+    NULL::float8 as coloc_h4,
+    NULL::float8 as r2,
+    NULL::integer as n_coloc_between_traits,
     ma.data_submission_id as data_submission_id,
     fs.id as signal1_id,
     NULL::integer as signal2_id