fix for spoligotype from bam

jodyphelan · Dec 26, 2024 · f8a5070 · f8a5070
1 parent 5a9644a
commit f8a5070
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/tbprofiler/spoligotyping.py b/tbprofiler/spoligotyping.py
@@ -5,6 +5,8 @@
 import logging
 
 def spoligotype(args):
+    if args.bam:
+        args.bam_file = args.bam
     if "bam_file" in vars(args) and args.bam_file:
         result = bam2spoligotype(args.bam_file,args.files_prefix,args.conf,threads=args.threads,max_mem=args.ram)
     elif args.read1: