Thanks @robert-vogel,

Btw, did you just replace the old option do_phasing with doPhasing? Do you have a more strong argument for this change other than being opinionated? We'd like to avoid breaking changes unless necessary.

Zilong.

Hi @Zilong-Li,

The update is just adding doPhasing to the STITCH.R script for using STITCH from the command line. The remaining changes were, for the most part, in service to that option. I changed the variable from snake case to camel case because it seemed that most of the variables presented to the user were in camel case, see lines 92-315 in the STITCH.R script. Personally, I have no preference in variable naming conventions, so-long as the convention is consistent.

If you prefer snake case for do_phasing, I am happy to make that update. I don't want to make any more work for you with such a trivial update.

best,

Robert

Ah, sorry I overlooked the CLI part in this PR. Would be appreciated if you can use snake case for do_phasing.

Thanks,
Zilong

No problem. I'll work on the update to snake case today.

Thanks,
Robert

Hi, sorry for my slow reply I'm on parental leave and have also been on vacation for most of the last three weeks.

The inconsistency in camel case vs snake case is probably mostly my fault as I've bounced around various settings that have used one or the other and haven't been consistent here. I don't think it matters much.

I guess a more key question - does the phasing work? I imagine I wrote this code many years ago, and I can't quite remember what I would have done, and how accurate it was? @robert-vogel have you tested it?

Hi @rwdavies, congratulations on your new family member (in response to parental leave)! The code runs smoothly, but I haven't yet computed the switch error rate on our data. I expect to do this in the next month or so, as I am trying to solve a different challenge. I'm happy to share the results with you once they are generated.

@Zilong-Li Still need to update the variable name case, I'll do that soon, just got busy with other stuff.

I just now got back to this. I updated the names as requested. If you, @Zilong-Li , didn't already add do_phasing to STITCH command line script, this may be of use.

Thank you Robert!