Commit 871a1838 authored by MARIJON Pierre's avatar MARIJON Pierre

correct typo

parent 942a9e5f
......@@ -164,8 +164,8 @@ class Parser:
def generate_gfa(self):
yield "H\tVN:Z:1.0"
for seq, length in self.__segments.items():
if not self.containment and seq in self.__containments:
# if not self.containment and seq in self.__containments:
# continue
yield "S\t{}\t*\tLN:i:{}".format(seq, length)
for (read_a, _, read_b, _), link in self.__links.items():
......@@ -256,8 +256,8 @@ def main(args):
parser.add_argument('paf', type=argparse.FileType('r'))
parser.add_argument('gfa', type=argparse.FileType('w'))
parser.add_argument("-c", "--remove-all-containement", action='store_true',
help="Remove all containement")
parser.add_argument("-c", "--remove-all-containment", action='store_true',
help="Remove all containment")
parser.add_argument("-i", "--remove-all-internal", action='store_true',
help="Remove all internal match")
......@@ -265,7 +265,7 @@ def main(args):
arg = vars(parser.parse_args(args))
paf = arg["paf"].name
gfa = arg["gfa"].name
rm_all_contain = arg["remove_all_containement"]
rm_all_contain = arg["remove_all_containment"]
rm_all_internal = arg["remove_all_internal"]
parser = Parser(not rm_all_contain, not rm_all_internal)
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