sgkit

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Wheels on macOS Python 3.10 failing

1

See https://github.com/pystatgen/sgkit/runs/7745453482?check_suite_focus=true The problem is that cyvcf2 wheels for macOS Python 3.10 are only available from version [0.30.16](https://pypi.org/project/cyvcf2/0.30.16/#files), but that is built with NumPy 1.23 which is incompatible with Numba....

tomwhite

Fix get_region_start to work with contig names that have colons and dashes.

6

Addresses issue #882.

d-laub

HLA contigs have colons and dashes in their names and I believe this isn't addressed by the `vcf_to_zarr` implementation, specifically the `get_region_start` function: https://github.com/pystatgen/sgkit/blob/d08feba59415fa502150ad1d052e5377cdb83a94/sgkit/io/vcf/vcf_reader.py#L94-L100 This causes a "too many values...

d-laub

Is there a diference between variables `dosage` and `call_dosage`

4

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...

timothymillar

Disable numba caching via environment variable

2

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...

timothymillar

Related: https://github.com/pystatgen/sgkit/blob/84a5f6e2872a2d2882d87590d68b378f79ce8600/setup.cfg#L45-L57

ravwojdyla

See #873 and #878

tomwhite

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...

timothymillar

Summary statistics IO and methods

7

The MRC IEU at Bristol has a [specification](https://github.com/MRCIEU/gwas-vcf-specification) for storing GWAS summary statistics in a VCF file. While I certainly have mixed feelings about using VCF files as a container...

hammer

`gwas_linear_regression` is sensitive to Dataset transposition

6

Hi, I am encountering an error when calling `gwas_linear_regression` on a transposed `Dataset`. Given that all the dimensions are labelled in a standardized way, it seems to me that this...

clwgg