Tim Millar
Tim Millar
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...
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.
Related to #1035. It looks like the code for `write_vcf` wasn't updated to use the new array variables [(line)](https://github.com/pystatgen/sgkit/blob/main/sgkit/io/vcf/vcf_writer.py#L415). I also can't see "filter_id" in variables.py.
This is currently only implemented for the diploid biallelic case. Generalizing it to the multiallelic case would require that the number of possible alleles at each variant is known. See...
The `write_vcf` function doesn't support float64 which makes sense given it's not supported by the VCF specification. However, manually converting float64 arrays to float32 is a bit of a pain,...
We don't currently have any IO functionality for pedigree formats. These are usually tabular but can be quite variable. We should document how to read in some generic examples and...