Shift correction improvements

[kemaleren]

• [x] print discarded sequences and the reason for the discard
• [ ] codon grouping with lookahead/behind
• [ ] use codon scoring matrix in out-of-frame regions.
• [ ] identify stutters
• [ ] possibly tolerate more errors in less conserved regions
• [ ] penalize early stop codons
• [ ] use base-wise quality scores.
• [ ] use bealign to do real codon alignment. possibly modify bealign to generate in-frame references.

[kemaleren]

Going to be fixed with rifraf anyways