fix for pilot VCFs

jodyphelan · Oct 31, 2024 · 847ca53 · 847ca53
1 parent a1b41f3
commit 847ca53
Showing 1 changed file with 2 additions and 3 deletions.
diff --git a/pathogenprofiler/vcf.py b/pathogenprofiler/vcf.py
@@ -223,10 +223,9 @@ def load_ann(
                 else:
                     if 'QNAME' in var.info:
                         freq = 1.0
-                    elif sv:
-                        freq = af_dict[alt]
                     else:
-                        raise NotImplementedError
+                        freq = af_dict[alt]
+
 
                 tmp_var = Variant(
                     chrom = chrom,