From 2df136ce49f2a0ac938e2dfdddfdd4e0ec1c9f7e Mon Sep 17 00:00:00 2001
From: zhengzhenxian <920596906@qq.com>
Date: Fri, 14 Jul 2023 15:51:03 +0800
Subject: [PATCH] update PL for refcall

---
 clair3/CallVariants.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/clair3/CallVariants.py b/clair3/CallVariants.py
index 18fd17a..5f98ad1 100644
--- 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