Tim Millar
Tim Millar
Hi, I'm having issue installing `iocaml` on ubuntu 16.04: ``` $ opam install iocaml The following actions will be performed: ∗ install iocaml 0.4.9 =-=- Gathering sources =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= [default] https://opam.ocaml.org/archives/iocaml.0.4.9+opam.tar.gz...
Are these duplicate variables? `call_dosage` seems to be more explicit with ndim=2 and the associated `call_dosage_mask` but isn't currently being used. Variable `dosage` doesn't specify dimensions and is used for...
Edit: related to #371 I've recently started experimenting with sgkit on a [SLURM cluster](https://jobqueue.dask.org/en/latest/generated/dask_jobqueue.SLURMCluster.html) which is working well with the exception of methods using `guvectorize` with `cache=True`. Calling these functions...
Implement the VanRaden genomic relationship matrix ([VanRaden 2008](https://www.sciencedirect.com/science/article/pii/S0022030208709901)). This is typically calculated from dosages for biallelic markers and has been generalized to autopolyploids (fixed ploidy). One consideration is the specification...
Related to #845. Estimation of inbreeding coefficients from pedigree data does not require computation of the full kinship matrix. [Hamilton and Kerr (2017)](https://pubmed.ncbi.nlm.nih.gov/29260268/) outline an approach to this which works...
sgkit stores genomic windows as the indices of their first and last variants within each window. This means that filtering variants (i.e. dropping some variants from the dataset) will invalidate...
Currently the windowed aggregation of statistics in `popgen.py` is hard-coded to use `np.sum` [[1](https://github.com/pystatgen/sgkit/blob/main/sgkit/stats/popgen.py#L108), [2](https://github.com/pystatgen/sgkit/blob/main/sgkit/stats/popgen.py#L275), [3](https://github.com/pystatgen/sgkit/blob/main/sgkit/stats/popgen.py#L566), [4](https://github.com/pystatgen/sgkit/blob/main/sgkit/stats/popgen.py#L1080)]. Would it be possible to make this aggregation optional or have a `span_normalise`...
Currently a lower ploidy sample appears to have missing alleles i.e. -2 is treated as -1. The the calls `[[0, 0, 1, 1], [0, 1, -2, -2], [0, 0, 1,...
I've finally had time to put together an example tetraploid and pseudo mixed-ploidy VCF example with some previously published potato data: https://github.com/pfrnz/Example-Tetraploid-Potato-VCF-PRJNA414303. Just make note of the issue in the...
It would be nice display a `call_allele_count` array in a more intuitive manner, similar to the `display_genotypes` function (#37). Scikit-allel does this nicely with its `GenotypeAlleleCountsArray` class which displays ordered...