--- a/hubArchiveCreator.py	Tue May 09 15:42:43 2017 -0400
+++ b/hubArchiveCreator.py	Wed May 31 11:35:16 2017 -0400
@@ -20,6 +20,7 @@
 from BedSimpleRepeats import BedSimpleRepeats
 from BedSpliceJunctions import BedSpliceJunctions
 from Bed import Bed
+from cytoBand import cytoBand
 from BigWig import BigWig
 from util.Fasta import Fasta
 from util.Filters import TraceBackFormatter
@@ -29,6 +30,7 @@
 from TrackHub import TrackHub
 from bigPsl import bigPsl
 from BedBlastAlignments import BedBlastAlignments
+from BigBed import BigBed
 
 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
 
@@ -55,6 +57,9 @@
     # Generic Bed (Blastx transformed to bed)
     parser.add_argument('--bed', action='append', help='Bed generic format')
 
+    #cytoBandIdeo
+    parser.add_argument('--cytoBand', action='append', help='Cytoband Track, using cytoBandIdeo.as')
+
     # BigPsl (blat alignment)
     parser.add_argument('--bigpsl', action='append', help='bigPsl format, using bigPsl.as')
 
@@ -70,6 +75,9 @@
     # Psl Management
     parser.add_argument('--psl', action='append', help='Psl format')
 
+    # BigBed Management
+    parser.add_argument('--bigbed', action='append', help='BigBed format')
+
     # TODO: Check if the running directory can have issues if we run the tool outside
     parser.add_argument('-d', '--directory',
                         help='Running tool directory, where to find the templates. Default is running directory')
@@ -124,6 +132,7 @@
     # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
     array_inputs_bam = args.bam
     array_inputs_bed_generic = args.bed
+    array_inputs_bed_cytoBand = args.cytoBand
     array_inputs_bed_simple_repeats = args.bedSimpleRepeats
     array_inputs_bed_splice_junctions = args.bedSpliceJunctions
     array_inputs_bigwig = args.bigwig
@@ -132,6 +141,7 @@
     array_inputs_psl = args.psl
     array_inputs_bigpsl = args.bigpsl
     array_inputs_bed_blast_alignments = args.bedBlastAlignments
+    array_inputs_bigbed = args.bigbed
 
     outputFile = args.output
 
@@ -152,6 +162,7 @@
     for (inputs, datatype_class) in [
                         (array_inputs_bam, Bam),
                         (array_inputs_bed_generic, Bed),
+                        (array_inputs_bed_cytoBand, cytoBand),
                         (array_inputs_bigwig, BigWig),
                         (array_inputs_bed_simple_repeats, BedSimpleRepeats),
                         (array_inputs_bed_splice_junctions, BedSpliceJunctions),
@@ -159,7 +170,8 @@
                         (array_inputs_gtf, Gtf),
                         (array_inputs_psl, Psl),
                         (array_inputs_bigpsl, bigPsl),
-                        (array_inputs_bed_blast_alignments, BedBlastAlignments)]:
+                        (array_inputs_bed_blast_alignments, BedBlastAlignments),
+                        (array_inputs_bigbed, BigBed)]:
         if inputs:
             all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))