Merge pull request #92 from szhan/handle_none_in_allele_list

Remove None when making alternate alleles string if in allele list
szhan · Jun 8, 2023 · c88d5ec · c88d5ec
2 parents 6db01a9 + adadf4b
commit c88d5ec
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/util.py b/src/util.py
@@ -80,7 +80,7 @@ def print_tsdata_to_vcf(
             # If the ts was produced by simulation,
             # there's no ref. sequence other than the ancestral sequence.
             REF = v.site.ancestral_state
-            alt_alleles = list(set(v.alleles) - {REF})
+            alt_alleles = list(set(v.alleles) - {REF} - {None})
             AA = v.site.ancestral_state
             ALT = ",".join(alt_alleles) if len(alt_alleles) > 0 else "."
             INFO = "AA" + "=" + AA