sgkit
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sgkit-dev
Scalable genetics toolkit
We have used Numba to accelerate CPU computations in sgkit for a long time - and to great effect. We have previously [discussed](https://github.com/sgkit-dev/sgkit/discussions/1224) trying JAX as an alternative to see...
The function `sgkit.window_by_position` fails if the input dataset has contigs that lack variant sites, throwing an `IndexError`. Traceback ```python IndexError Traceback (most recent call last) Cell In[36], line 1 ---->...
This was originally reported in #1247 and a temporary pin introduced in #1248. I've opened this to track the issue so we can remove the pin.
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Citation
Hello! I'm not sure if this is already indicated elsewhere, but how do we cite the package?
We should encourage people to start using bio2zarr and vcztools for plink conversion, rather than the functions in sgkit.
See https://github.com/sgkit-dev/bio2zarr/issues/391 for details. It's less obviously incorrect here than in bio2zarr where we're striving for compatability, but it's still a surprising choice which should be documented if there's a...
Here's my code: ``` data_path = "tests/data/plink/" bed_path = data_path + "plink_sim_10s_100v_10pmiss.bed" fam_path = data_path + "plink_sim_10s_100v_10pmiss.fam" bim_path = data_path + "plink_sim_10s_100v_10pmiss.bim" # print(bed_path) # print(fam_path) sg_ds = sgkit.io.plink.read_plink( bed_path=bed_path,...
We're pinning to the git version of bio2zarr in a few places, I think we can just use the latest from pypi now.