Nucleotide alignment with invalid nucleotide "X"

[Changwanseo]

• Environment: UFCG 1.0.3, conda installed version, ubuntu 20.04
• Steps that I've done:

0. Prepare input file
   /tmp
   GCA_024703775.1.fna
   .... (many other genome fna files)

1. Call ucg file with "profile"
   ufcg profile -i ./tmp 0o ./101_ufcg_profile -t 32 -v --developer --force 1

2. Align with ufcg
   ufcg align -i ./101_ufcg_profile -o ./201_ufcg_align_nuc -l acc -a nucleotide -n align -l strain -t 24

• Problems
  The resulting alignment includes nucleotide "X", which makes many other programs (such as MAFFT without sequence designation, or geneious) to recognize alignment file as protein alignment. It would be better alignment to change "X" to "N" if "-a nucleotide" flag included

[endixk]

Current version has a flawed nucleotide sequence extraction process in which all lowercase bases from the backward strands are converted into the alphabet X.

Commit fe699d1 will not only fix this issue, but also improve the speed of the reverse complement sequence computation in general. I will soon make a new release including this update.