Peter Ralph
Peter Ralph
I'm happy to do that; I think the main question is what to call the function; weigh in over at #2725.
`legacy` will still give you 0s: https://github.com/tskit-dev/tskit/blob/main/python/tskit/vcf.py ... and it looks like [a workaround](https://github.com/tskit-dev/tskit/blob/main/python/tskit/vcf.py#L82) is to pass `position_transform = lambda x: 1 + np.round(x)` to [position_transform](https://tskit.dev/tskit/docs/latest/python-api.html#tskit.TreeSequence.write_vcf)? But, this is very...
That's a good suggestion - provide the solution in the docs.
Correct me if I'm wrong, but I don't think that the issue is the usual 0-or-1-based indexing. If it was, then "gene X extends from position 1000 to position 1200"...
As I said over at that PR, I like this solution: there's an informative error message that provides the solution.
> I meant to say, I'm happy to dig into this and open a PR with a fix. I think it will be pretty simple. Awesome! A nice way to...
This one is also not blocking - however, I do risk losing changes I made in SLiMgui but forgot about, so it's somewhat more worrisome.
I'm using GUI version 5.3, Qt 5.15.13, Git-SHA-1 f872f3df812. I could upgrade to Qt6 if you like?
I have not worked out the details, but the basic idea is that the PCs are the eigenvectors of the genetic covariance matrix, and modern iterative methods (like Krylov methods)...
🎉 Closed in #3008 and other places!