Defined missing variable

Multiscale-Genomics · May 9, 2017 · 3edbc05 · 3edbc05
1 parent 3434148
commit 3edbc05
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/tool/bed_indexer.py b/tool/bed_indexer.py
@@ -110,7 +110,7 @@ def bed2bigbed(self, file_sorted_bed, file_chrom, file_bb):
                        "bed2bigbed: Could not process files {}, {}.".format(*input_files)))
         
         """
-        command_line = 'bedToBigBed ' + file_sorted_bed + ' ' + file_chrom + ' ' + file_bb
+        command_line = 'bedToBigBed  ' + file_sorted_bed + ' ' + file_chrom + ' ' + file_bb
         args = shlex.split(command_line)
         p = subprocess.Popen(args)
         p.wait()
@@ -294,6 +294,8 @@ def run(self, input_files, metadata):
 
         assembly = metadata['assembly']
 
+        output_metadata = {}
+
         # handle error
         if not self.bedsort(bed_file, bed_sorted_file):
             output_metadata.set_exception(