Louis BECQUEY

Fix: command line arguments to pass to cmalign and stats

......@@ -1225,12 +1225,12 @@ class Pipeline:
path_to_seq_data + "realigned",
path_to_seq_data + "rfam_sequences"])
self.REUSE_ALL = True
elif opt == "cmalign-opts":
self.ALIGNOPTS = arg
elif opt == "cmalign-rrna-opts":
self.RRNAALIGNOPTS = " ".split(arg)
elif opt == "stats-opts":
self.STATSOPTS = " ".split(arg)
elif opt == "--cmalign-opts":
self.ALIGNOPTS = arg.split(" ")
elif opt == "--cmalign-rrna-opts":
self.RRNAALIGNOPTS = arg.split(" ")
elif opt == "--stats-opts":
self.STATSOPTS = arg.split(" ")
elif opt == "--all":
self.REUSE_ALL = True
self.USE_KNOWN_ISSUES = False
......