Minor fixes

python/obitools3/commands/alignpairedend.pyx

@@ -28,14 +28,14 @@ def addOptions(parser):
  
     group.add_argument('-f', '--forward-reads',
                      action="store", dest="alignpairedend:forward",
-                     metavar="<FILENAME>",
+                     metavar="<URI>",
                      default=None,
                      type=str,
                      help="URI to the forward reads")
 
     group.add_argument('-r', '--reverse-reads',
                      action="store", dest="alignpairedend:reverse",
-                     metavar="<FILENAME>",
+                     metavar="<URI>",
                      default=None,
                      type=str,
                      help="URI to the reverse reads")
@@ -56,6 +56,8 @@ def addOptions(parser):
                      help="Minimum score for keeping alignments")
 
 
+# TODO declarations, cdef, imports
+
 la = QSolexaReverseAssemble()
 ra = QSolexaRightReverseAssemble()
 def buildAlignment(Nuc_Seq_Stored direct, Nuc_Seq_Stored reverse):