sgkit issues

MemoryError: Allocation failed (probably too large) with ped.compute()

7

Hi, I am running a big simulation with a million people and I'd like to calculate the genealogical relatedness between them. I tried running sgkit and unfortunately, when I hit...

fouerghi

Move docs to sgkit.dev

We might even want to make a full website as part of this switch? Either way I'll look into Cloudflare's DNS admin interface soon...

hammer

documentation

`vcf_to_zarr` raises error instead of truncating INFO fields of length `R`

3

In `vcf_to_zarr`, specifying `max_alt_alleles` as smaller than the actual maximum is meant to truncate the alleles dimension (with a warning). However, if there is an INFO field with length `R`...

timothymillar

bug

IO

read_plink returns bytes for variant_alleles not unicode

There's no good reason for returning bytes rather than utf8 unicode strings I think --- it can only lead to bugs in user code and inconsistencies in string handling (anyone...

jeromekelleher

bug

Partial changes for VCF Character S->U

Updates for vcf-zarr spec change: https://github.com/pystatgen/vcf-zarr-spec/issues/14 Almost working, I think the main issues remaining are in the round-trip tests. Nobody uses Character columns in the real world I think, so...

jeromekelleher

Mixed-ploidy VanRaden GRM

A couple of recent publications generalize the VanRaden estimator to mixed-ploidy populations. - [Batista et al 2022](https://link.springer.com/article/10.1007/s00122-021-03994-w) - [Bilton et al 2024](https://link.springer.com/article/10.1007/s00122-024-04568-2) The later goes into the derivation in more...

timothymillar

enhancement