update PL for refcall

HKU-BAL · Jul 14, 2023 · 2df136c · 2df136c
1 parent 4f3df55
commit 2df136c
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/clair3/CallVariants.py b/clair3/CallVariants.py
@@ -1384,7 +1384,10 @@ def compute_PL(genotype_string, genotype_probabilities, gt21_probabilities, refe
             gt21_prob_index = gt21_enum_from_label(gt21_label)
         except:
             #skip N positions
-            return [990] * len(genotypes[alt_num])
+            if alternate_base == ".":
+                return [990]
+            else:
+                return [990] * len(genotypes[alt_num])
         genotype_prob_21 = gt21_probabilities[gt21_prob_index]
 
         # obtain the genotype probability from 3 zygosity