only mask sites that aren't gapped
@@ -48,6 +48,7 @@ if __name__ == '__main__':
seq_list = list(start + middle + end)
if args.mask_sites:
for site in args.mask_sites:
+ if seq_list[site-1]!='-':
seq_list[site-1] = "N"
record.seq = Seq("".join(seq_list))
write_sequences(record, outfile)
