Clean up bowtie script

bowtie

@@ -38,31 +38,19 @@ def main():
 
     parser = argparse.ArgumentParser()
 
-    group = parser.add_mutually_exclusive_group()
-    group.add_argument('-b', '--build', action='store_true')
-    group.add_argument('-i', '--inspect', action='store_true')
-
     parser.add_argument('--verbose', action='store_true')
     parser.add_argument('--debug', action='store_true')
     parser.add_argument('--large-index', action='store_true')
-    parser.add_argument('--index', type=str)
 
     # parse the args specific to the wrapper script
     # all other args will be passed verbatim to bowtie
     args, bowtie_args = parser.parse_known_args()
 
-    action = 'align'
-    if args.inspect:
-        action = 'inspect'
-    elif args.build:
-        action = 'build'
-
     logging.basicConfig(level=logging.ERROR,
                         format='%(levelname)s: %(message)s'
                         )
-    bin_name            = 'bowtie' + '-' + action
-    bin_s               = 'bowtie-%s-s' % action
-    bin_l               = 'bowtie-%s-l' % action
+    bin_s               = 'bowtie-align-s'
+    bin_l               = 'bowtie-align-l'
     idx_ext_l           = '.1.ebwtl'
     idx_ext_s           = '.1.ebwt'
     ex_path             = os.path.dirname(os.path.realpath(__file__))
@@ -75,28 +63,12 @@ def main():
     if args.large_index:
         bin_spec = os.path.join(ex_path, bin_l)
 
-    if args.index:
-        if args.build:
-            delta = 200
-            small_index_max_size = 4 * 1024 ** 3 - delta
-            tot_size = sum([os.stat(fn).st_size
-                            for fn in args.index.split(',')
-                            if os.path.exists(fn)])
-
-            if tot_size > small_index_max_size:
-                bin_spec = os.path.join(ex_path, bin_l)
-        else:
-            if not os.path.exists(arg + idx_ext_s)\
-                    and os.path.exists(args.index + idx_ext_l):
-                bin_spec = os.path.join(ex_path, bin_l)
-        bowtie_args.insert(0, args.index)
-    else:
-        for arg in bowtie_args:
-            if arg[0] == '-':
-                continue
-            if not os.path.exists(arg + idx_ext_s)\
-                    and os.path.exists(arg + idx_ext_l):
-                bin_spec = os.path.join(ex_path, bin_l)
+    for arg in bowtie_args:
+        if arg[0] == '-':
+            continue
+        if not os.path.exists(arg + idx_ext_s)\
+           and os.path.exists(arg + idx_ext_l):
+            bin_spec = os.path.join(ex_path, bin_l)
 
     if args.debug:
         bin_spec += '-debug'