--- a/picard_wrapper.py	Mon Jun 16 17:38:15 2014 -0400
+++ b/picard_wrapper.py	Mon Jul 21 15:24:40 2014 -0400
@@ -804,7 +804,7 @@
     elif pic.picname == "DownsampleSam":
         cl.append('I=%s' % opts.input)
         output_string = opts.output
-        if opts.datatype == 'sam':
+        if opts.output_format == 'sam':
             output_string = output_string + ".sam"
         cl.append('O=%s' % output_string)
         if float(opts.probability) > 0:
@@ -812,9 +812,8 @@
         if float(opts.seed) > 0:
             cl.append('RANDOM_SEED=%s' % opts.seed)
         stdouts,rval = pic.runPic(opts.jar, cl)
-        if opts.input.endswith(".sam"):
-            renamed_output = output_string.replace(".sam", "")
-            os.rename(output_string,renamed_output)
+        if opts.output_format == 'sam':
+            os.rename(output_string, opts.output)
 
     elif pic.picname == 'MeanQualityByCycle':
         isPDF = 'MeanQualityByCycle.pdf'