Aidan Lakshman

Thanks for the callout -- this is fixed in https://github.com/Bioconductor/Biostrings/pull/110. Just going to do some testing to make sure nothing weird happens before merging.

Thanks for the callout, and apologies for the slow turnaround--this is fixed in #111. The return values in the new version should be consistent with inputs of length > 0:...

This is fixed in https://github.com/ahl27/Biostrings/tree/wildcardAA, will be put up for PR after #97 is merged

I'm not sure, it's quite a bit more work than I had initially expected--`XStringSet`s assume single byte character input, so we'd have to rewrite quite a bit of stuff to...

On second thought, it could be pretty simple to just add an optional argument like `useThreeLetterCodes=FALSE` to the `AAString` method, and then if true to call a preprocessing function like...

Sorry for the slow follow up--I think for now I'm going to leave this as unimplemented. I'm not sure it makes sense to change the constructor `AAString` method to have...

I added this to the `TODO` file so I don't forget about it in the future--I'll look into revisiting this when I have more bandwidth and the higher priority tasks...

@hpages pinging to follow up on conversation from the other PR--is this also something that we need to merge?

Yep, I'll take a look at it tomorrow--thanks for the ping!

You can send it to [email protected]'s been a while since I read through this bug report, so I can reread through it tomorrow. It's been on my list for a...