Jeff Hammerbacher

Fix hlarp hack

1

Uncovered during the offsite, this ain't right https://github.com/hammerlab/biokepi/blob/master/src/bfx_tools/hlarp.ml#L31-L36 cc @rleonid @julia326

https://github.com/amplab/snap

Add support for BASSOVAC

3

https://github.com/ding-lab/bassovac

More flexible "Invitees can schedule"

8

Thanks for the great open source product! I would like to be able to limit the days on which invitees can schedule a meeting with more flexibility than is currently...

Change organization and project name expansion

3

We [decided](https://github.com/pystatgen/sgkit/discussions/1166) to rename the organization to `sgkit-dev` and to expand `sgkit` to "Scalable genetics toolkit". We should make the corresponding changes and make sure all project resources work.

Sequential VCF parsing

1

@jeromekelleher to bring over https://github.com/pystatgen/sgkit-publication/pull/94, motivated by https://github.com/pystatgen/sgkit/issues/1168. Related to https://github.com/pystatgen/sgkit/issues/1130.

read_plink from cloud storage

3

We are able to read VCF files from [cloud storage](https://pystatgen.github.io/sgkit/latest/vcf.html#cloud-storage) thanks to support in `htslib` for some functions and `fsspec` for others. For PLINK BED files, I don't believe we...

How do I... additions

3

Operations I find myself doing regularly - add new sample metadata? - add new variant metadata? - merge 2 datasets with separate chromosomes/contigs into 1 dataset? We have a TODO...

Let's address by having validation tests be "as of" the time of implementation rather than trying to validate against current implementations. @ravwojdyla indicated some interest in this one

How do I add a new sample or variant data variable from a file?

1

We have [How do I define a new variable based on others?](https://pystatgen.github.io/sgkit/latest/how_do_i.html#define-a-new-variable-based-on-others), and we have [Adding column fields](https://pystatgen.github.io/sgkit/latest/examples/gwas_tutorial.html#adding-column-fields) in the GWAS docs. I think we could expand this documentation to...