20240722 developer call notes

[tomwhite]

20240722

Pre-notes

• Notes from previous meeting

PRs

Issues

Discussions

• Vcztools planning
• Zarr v3 in bio2zarr
• scverse+sgkit

Notes

Attendees

1. Jeff Hammerbacher
2. Tom White
3. Jerome Kelleher
4. Ben Jeffery

Discussion

Vcftools

• Agree to move to sgkit-dev. JK will do it soon.
• Need to list what commands to prioritise
  • JK: filtering options (GeL cookbook)
• JH: which commands are difficult to implement? Pull those forward
• TW: Which datasets should we be using?
  • JK: 1K genomes chr2 or 20
• TW: Cubed work on single machine is relevant to vcztools: Single machine tracking issue cubed-dev/cubed#514
• TW: scverse on Xarray meeting with Jan Engelmann
• Zarr v3 work might be unblocked by Ryan A? Run tests against Zarr 3 bio2zarr#254 points to Add string and bytes dtypes plus vlen-utf8 and vlen-bytes codecs zarr-developers/zarr-python#2036 which makes v3 backwards compatible with v2. Arrow might be the future though.
• TW: HPC work in Cubed has had lots of activity recently (about suggested approaches), e.g. Dragon from HPE HPC executor cubed-dev/cubed#467

Vcf spec

• JK: Header - identify which header fields are redundant and don’t store them. E.g. sample IDs.
  • Bio2zarr and vcztools implement first.
  • Identify the fields first.

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