Option to ignore shared substitutions

[ktmeaton]

• I've been experimenting with a flag --ignore-shared that ignores positions that are shared (have the exact same nucleotide) across all parents/examples.
• I like this option because it makes the breakpoints visually clearer, as there's a direct color change (red -> green) rather than having the intermediate shared positions (red -> white -> green)
• For testing, a nextclade fasta alignment of XM-like recombinants (public on genbank): XM.txt

1. Do you think this is scientifically sound for reporting? And if so,
2. Would you be interested in a PR if I tidy up the code?

Default Output:

python3 sc2rf.py XM.fasta --ansi --unique 1

Proposed Option:

python3 sc2rf.py XM.fasta --ansi --unique 1 --ignore-shared