Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ARG conversion functionality #44

Open
hyanwong opened this issue Nov 13, 2022 · 0 comments
Open

ARG conversion functionality #44

hyanwong opened this issue Nov 13, 2022 · 0 comments

Comments

@hyanwong
Copy link
Member

hyanwong commented Nov 13, 2022

Over in https://github.com/tskit-dev/what-is-an-arg-paper/blob/main/argutils/convert.py we have some utilities to convert KwARG and ARGweaver files into ARG-format tree sequences. There is also a conversion-from-ARGweaver function associated with Guo and Rassmussen's SCAR which has simply lifted the code I wrote in https://github.com/mcveanlab/treeseq-inference/blob/master/src/ts_ARGweaver.py.

I think it would be useful, rather than reusing random bits of untested code, to have some of these in tsconvert. One question is whether we use the 2-RE-node representation (I guess yes, as this allows us to calculate the likelihood).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant