bugfix

jodyphelan · Oct 17, 2024 · 7d8bc7e · 7d8bc7e
1 parent 104116c
commit 7d8bc7e
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/scripts/combine_vcf_variants.py b/scripts/combine_vcf_variants.py
@@ -202,8 +202,10 @@ def has_md_tag(bam):
             variant.info['SAF'] = hap_fwd
             variant.info['SAR'] = hap_rev
         if 'ADF' in var.samples[0]:
-            var.samples[0]['ADF'] = hap_fwd
-            var.samples[0]['ADR'] = hap_rev
+            print(var)
+            print(hap_fwd,hap_rev)
+            var.samples[0]['ADF'] = (ref_fwd,hap_fwd)
+            var.samples[0]['ADR'] = (ref_rev,hap_rev)
         if 'AD' in variant.samples[0]:
             variant.samples[0]['AD'] = [dp - count, hap_fwd + hap_rev]