add check for NaNs in burdens or genotypes

PMBio · Oct 30, 2024 · cbf432d · cbf432d
1 parent e11a44c
commit cbf432d
Showing 1 changed file with 9 additions and 0 deletions.
diff --git a/deeprvat/deeprvat/associate.py b/deeprvat/deeprvat/associate.py
@@ -474,6 +474,15 @@ def make_regenie_input_(
                     axis=1,
                 )
 
+                # TODO: Sanity check, remove in future (?)
+                burden_nan_count = np.sum(np.isnan(this_burdens))
+                genotypes_nan_count = np.sum(np.isnan(genotypes))
+                if burden_nan_count or genotypes_nan_count:
+                    logger.warning(
+                        f"Found NaNs in data for gene {i} ({ensgids[i]}): "
+                        f"{burden_nan_count=}, {genotypes_nan_count=}"
+                    )
+
                 f.add_variant(
                     varid=varid,
                     rsid=varid,