Jerome Kelleher

Stuff in evaluation.py is basically developer utilities, so we don't need to worry too much.

I think they're all still marked as samples (we probably OR the flags with TSK_NODE_IS_SAMPLE) but I don't know off the top of my head. Should be easy enough the...

Sounds like a good idea to me. Some quick thoughts: > - inconsistencies in the references across tables These are checked when a tree sequence is loaded in tskit [here](tsk_table_collection_check_integrity)....

This could be done, I would imagine, but we'd need some way of outputting VCF INFO data. I've opened an issue on tskit to track this: https://github.com/tskit-dev/tskit/issues/434

I'm afraid I don't have that information available @XiaoleiZ, sorry. It would be a version that was current at the time the preprint was release, so Nov 2018. This code...

Sounds good to me.

requirements.txt is used by pip (and other tools) to specify requirements. It can be used like ``pip install -r requirements.txt``. This is a reason that it would have been nice...

Just adding my +1 to @tomwhite's comment above. Strings are crucial for supporting genetic variation data, which there is an awful lot of, and Zarr would be amazing for. See...

I agree having exhaustive feature completeness scores would be quite a chore, and very hard to keep up to date. What's not obvious from the current list though is that...

Thanks for the update @alimanfoo! I was thinking of submitting a talk for the [Research Software Engineers conference](https://rse.ac.uk/conf2019/call-for-submissions/); I was at the conference last year, and I'm sure there will...