Add -au/-ao options to argparser #251 #244

(still need to make them do stuff)

graph_collator/collate.py

@@ -72,6 +72,14 @@
     help="file containing bicomponent information for the assembly graph" + \
         " (will be generated using the SPQR script in the output directory" + \
         " if not passed)")
+parser.add_argument("-au", "--assumeunoriented", required=False, default=False,
+        action="store_true", help="assume that input GML-file graphs are" + \
+            " unoriented (default for GML files is assuming they are" + \
+            " oriented); this option is unfinished")
+parser.add_argument("-ao", "--assumeoriented", required=False, default=False,
+        action="store_true", help="assume that input LastGraph-/GFA-file" + \
+            " graphs are oriented (default for LastGraph/GFA files is" + \
+            " assuming they are unoriented); this option is unfinished")
 args = parser.parse_args()
 asm_fn = args.inputfile
 output_fn = args.outputprefix
@@ -81,6 +89,8 @@
 preserve_xdot = args.preservexdot
 overwrite = args.overwrite
 bicmps_fullfn = args.bicomponentsfile
+assume_unoriented = args.assumeunoriented
+assume_oriented = args.assumeoriented
 
 try:
     os.makedirs(dir_fn)