Support `U` as `T` for IUPAC codes

[nh13]

Would it be possible to encode Us as Ts with Iupac codes? See: https://www.bioinformatics.org/sms/iupac.html. I can convert them on my side, but wanted to check here.

[jeff-k]

Hi @nh13, yeah this would be good to have. What did you have in mind?

Some options I was mulling over are:

• parse a U as a T in the existing Iupac module but not preserve which of those it was when we display it (default to T),
• use a full 8-bit IUPAC module that encodes U/T separately,
• make a copy of the Iupac module specifically for RNA,
• add an associated type or use a trait that marks whether the Codec is for Dna or Rna

The last option would leverage the type system and wouldn't add any additional size to the sequence objects, which is in line with the project's goals but risks getting complicated.

I'm also thinking of an Rna codec that's virtually identical to Dna:

pub enum Rna {
    A = 0b00,
    C = 0b01,
    G = 0b10,
    U = 0b11,
}

and then work out a nicer refactoring of the two modules to eliminate the redundant code. This might favour the fourth option.

If we started with the first or second option for codec::Iupac we could add explicit conversions into either Dna or Rna sequences, so the user could at least control how the sequence is represented.

What do you think? I don't have any immediate applications for this and I suppose having a real life use-case would be a fair place to start.