Check if outfile

nriddiford · Feb 14, 2018 · f3a28b7 · f3a28b7
1 parent 13df0d1
commit f3a28b7
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/svSupport/merge_bams.py b/svSupport/merge_bams.py
@@ -5,7 +5,7 @@ def merge_bams(out_file, bams):
 
     for bam_file in bams:
         pysam.index(bam_file)
-        
+
     in_files = ', '.join(bams)
     print("Merging bam files %s into '%s'") % (in_files, out_file)
     merge_parameters = ['-f', out_file] + bams
@@ -15,4 +15,5 @@ def merge_bams(out_file, bams):
         os.remove(bp_file)
         os.remove(bp_file + ".bai")
 
-    pysam.index(out_file)
+    if out_file:
+        pysam.index(out_file)