Gather more variant definitions and helper functions

[DBecker7]

Part of my work involves comparing the results based on different definitions of variants. It would be nice to standardize this process.

• Constellations
  • Currently implemented, with a lot of AA parsing within the function. AA parsing could be moved to a separate function that would work for other definitions.
• Usher barcodes
  • Implemented.
• Usher barcodes with GISAID
  • Easy to add to current function
• Covariants.org
  • Defined via python code, which will take some interesting parsing scripts.
• Public Health England
  • Constellations AA parsing (above) will be very helpful here.
• outbreak.info (R package)
  • Add the R package as an optional dependency, then parse to consistent format.
• LAPIS API (which is maintained/used by cov-spectrum.org)
  • Has an R package, which could also be added as an optional dependency.

This is not a requirement for the current contract. Do not work on this unless all other issues are complete.

[DBecker7]

LAPIS API requires an API key, which I do not know how to obtain.