Tom White

Suggested by @benjeffery here: https://github.com/pystatgen/sgkit/pull/1054#pullrequestreview-1360645992 Do the same for `filters` and `contig_lengths`.

Alternative execution engines for VCF conversion

5

VCF to Zarr conversion is an embarrassingly parallel process that currently uses Dask Delayed to schedule tasks. It would be fairly easy to make it possible to run on any...

Benchmarks have stopped working

3

Stopped working about 5 days ago: https://github.com/pystatgen/sgkit/actions/workflows/benchmark.yml

I've been thinking about how we could run (parts of) sgkit on Cubed (#908). One thing that would help is using [`xarray.map_blocks`](https://docs.xarray.dev/en/stable/generated/xarray.map_blocks.html#xarray.map_blocks) (or [`xarray.apply_ufunc`](https://docs.xarray.dev/en/stable/generated/xarray.apply_ufunc.html)) instead of [`dask.array.map_blocks`](https://docs.dask.org/en/stable/generated/dask.array.map_blocks.html), since the Xarray...

When Zarr variable chunking ([ZEP 3](https://zarr.dev/zeps/draft/ZEP0003.html)) is available we would be able to write partitions of a VCF directly into Zarr chunks that vary in size along the variants dimension....

There is a new plan to bring Zarr up to date with the V3 spec over the next few months (see https://github.com/zarr-developers/zarr-python/discussions/1480). This issue is to run sgkit tests against...

This was deprecated in #1054, and should be removed in a future release. Similarly for `filters` and `contig_lengths`.

Make sample_id from plink reader unique

4

Currently `read_plink` maps the IID from the fam file to sgkit's `sample_id`. However, IID is only unique within the family ID (FID), so there is the potential for conflicts. (I...

See #1019

Improve control over float formatting in VCF writer

1

Follow on from discussion in #953. Get the round trip tests to work as far as possible. Part of #924