--- a/ALFA/ALFA_wrapper.py	Sun Dec 18 09:50:39 2016 -0500
+++ b/ALFA/ALFA_wrapper.py	Thu Dec 21 09:29:26 2017 -0500
@@ -54,6 +54,10 @@
     n = len(reads_list)
     if n%2 != 0:
         exit_and_explain('Problem with pairing reads filename and reads label')
+    if format == 'bam':
+        input2_args = '--bam'
+    elif format == 'begraph':
+        input2_args = '--bedgraph'
     input2_args='-i'
     k = 0
     reads_filenames = [''] * (n/2)
@@ -66,8 +70,6 @@
             reads_labels[k] = 'sample_%s' % str(k)
         input2_args='%s "%s" "%s"' % (input2_args, reads_filenames[k], reads_labels[k])
         k += 1
-    if format == 'bedgraph':
-        input2_args = input2_args + ' --bedgraph'
     return input2_args, reads_filenames, reads_labels
 
 def redirect_errors(alfa_out, alfa_err):