James Bonfield

Sadly no. It's something badly in need of work, but it's a complex task unless it's parallelised as above by dividing up into regions (and even then it's not trivial...

This is one of those things which just becomes akward once hard clipping is used. We could state that if hard clipping is to be used then the `N` notation...

One omission from bai, csi and crai is any way to tell if they're in sync with the associated file. If we were designing formats from scratch (that have separate...

Agreed it's not ideal and we probably shouldn't be starting from here. However computing a checksum has a *huge* CPU cost while checking headers match does not. Of course it's...

That's fine - I can accept that as an order in which things are done. Yes I think there are problems with the spec which haven't been spotted as no...

The TeX is invalid at the moment, meaning a PDF cannot currently be produced. I'm not a TeX expert, but it looks like you need eg `\vfifteen` instead of `\v15`...

The version in https://github.com/jkbonfield/hts-specs/tree/strict builds now, but needs a lot of formatting still. I'm not planning on doing this myself - this was just a test to see how to...

One other thought here, we know we can add our own additional meta-information lines. However as these are not formally defined, I assume *all* keys are therefore mandatory quoted (even...

The problem here is you have an individual sequence that is huge, which stats was never designed to cope with. It is overflowing the "int" data type. The above error...

The addition of this feature was a user request to track all stages of a pipeline, including file format changes which view is normally used for. Conversely, the adhoc debugging...