--- a/BedSimpleRepeats.py	Wed Jul 20 12:29:08 2016 -0400
+++ b/BedSimpleRepeats.py	Thu Jul 21 05:58:51 2016 -0400
@@ -10,40 +10,26 @@
 
 
 class BedSimpleRepeats( Datatype ):
-    def __init__( self, input_bed_simple_repeats_false_path, data_bed_simple_repeats,
-                 input_fasta_file, extra_files_path, tool_directory ):
+    def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats):
 
-        super(BedSimpleRepeats, self).__init__(
-                input_fasta_file, extra_files_path, tool_directory
-        )
+        super(BedSimpleRepeats, self).__init__()
 
         self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path
         self.name_bed_simple_repeats = data_bed_simple_repeats["name"]
         self.priority = data_bed_simple_repeats["order_index"]
 
         sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
-        twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
-        chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
 
         # Sort processing
         subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
 
-        # TODO: Regroup in an mother class which handles the Chrom.sizes creation with Gff3 and Gtf
-        # Generate the chrom.sizes
-
-        subtools.twoBitInfo(self.twoBitFile.name, twoBitInfoFile.name)
-
-        # Then we get the output to inject into the sort
-        # TODO: Check if no errors
-        subtools.sortChromSizes(twoBitInfoFile.name, chromSizesFile.name)
-
         # bedToBigBed processing
         # TODO: Change the name of the bb, to tool + genome + .bb
         trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
         myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
         auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as'))
         with open(myBigBedFilePath, 'w') as bigBedFile:
-            subtools.bedToBigBed(sortedBedFile.name, chromSizesFile.name, bigBedFile.name,
+            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name,
                                  typeOption='-type=bed4+12',
                                  autoSql=auto_sql_option)