sgkit
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sgkit-dev
Scalable genetics toolkit
This is an umbrella issue to track the work needed to run sgkit on [Cubed](https://github.com/tomwhite/cubed). This is possible because Cubed exposes the [Python array API standard](https://data-apis.org/array-api/latest/) as well as [common...
Currently most of the pedigree methods for estimating kinship, inbreeding and etc. require that the parent dimension is of length two. I've run into this limitation when working with pedigree...
Fixes #874 I've tried to preemptively make this function suitable for additional estimators if/when required. One point I'm unsure on is if we should have a default for `ancestral_frequency` based...
Related to #868 and #893 I'm wondering if we can start to check dimension names of variables without being too heavy handed by using warnings. This could potentially avoid manual...
ref #609 Add mean impute function for `call_dosage`, `call_genotype`, and `call_genotype_probability`
See discussion in #888 Most methods within `popgen.py` are automatically applied over windows and default to variants if the dataset has not been windowed. It would be useful to optionally...
- [x] Fixes #1194 Leaving `NUMBA_DISABLE_JIT=1` for `test_pedigree.py` which contains many jitted functions.
Turning off the numba cache seems to cause our CI builds to fail when running tests in NOJIT mode (which we use to get coverage of jitted functions). Seems quite...
This is causing persistent problems, with cryptic segfaults being really really hard to debug with Dask (I just lost a whole morning to it!). We have to turn off the...