Allow suppression of |(reverse complement) suffix in header of alignment output

[corneliusroemer]

When --retry-reverse-complement is passed and a reverse complement is aligned, we add a |(reverse complement) suffix to the FASTA header of the affected sequence.

This can cause issues when matching sequences with metadata, as some scripts within augur expect the entire header to be unchanged.

It would be helpful if we offered the option to suppress the suffix. Workaround for now is for example a sed one-liner, though it's not so ergonomic to do this for all translations as well.

[ivan-aksamentov]

That's exactly why I was against adding a suffix back then! :)

On the other hand, we emit results for another sequence, against usual expectations, and it's not manifested particularly loud.

Could you please propose how that feature would look like?

[corneliusroemer]

Maybe something like: --reverse-complement-suffix true/false or alternatively --no-reverse-complement-suffix/--add-reverse-complement-suffix