20240819 developer call notes

[tomwhite]

20240819

Pre-notes

• Notes from previous meeting

PRs

Issues

Discussions

Notes

Attendees

1. Jeff Hammerbacher
2. Tom White
3. Will Tyler

Discussion

• Vcztools - Will has finished initial implementation
  • TW: any expressions that can’t be parsed using pyparsing?
  • WT: think all should be possible, but haven’t proved it
  • JH: we used PEG in an older project: https://github.com/hammerlab/cycledash/blob/master/grammars/querylanguage.pegjs
  • TW: remaining work is basically query, and header stuff
• JH: PGEN format - came up with NIH AllOfUs
  • https://github.com/chrchang/plink-ng/blob/master/pgen_spec/pgen_spec.pdf
  • AllOfUs use this
  • Optimization for storage, worth looking at for working with BioBanks
  • https://www.biorxiv.org/content/10.1101/2024.04.11.589062v1
  • Julia implementation (!) https://github.com/OpenMendel/PGENFiles.jl
• JH: Tensorstore afdist Tensorstore afdist vcf-zarr-publication#154
  • Use C++ and TS to use https://saigegit.github.io/SAIGE-doc/
• TW: scaling sgkit methods
  • Run on Cubed #908 (comment)
  • Will explore Zarr and JAX too

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