groupGenes needs updated naming and to figure out the locus list.

[Cole Jensen]

There is a filtering step/locus check if the data is identified as single cell data. However, during this check the locus values is being compared against a set list of possible loci within the function (just search “IGI” and you’ll find it). We need to decide if that’s the best way to check for a valid locus or not.

[Jason Vander Heiden]

You could get this from the AIRR Schema (in the airr R package), specifically the valid enum values in Rearrangement.locus:

https://github.com/airr-community/airr-standards/blob/master/specs/airr-schema.yaml#L3184

(“IGI” is a fish light chain locus, so it’d be grouped with IGK and IGL.)

[ssnn]

shazam uses a similar check, https://bitbucket.org/kleinstein/shazam/src/edf09a658fc60b83a4aac48b778edefc10b3a3cf/R/DistToNearest.R#lines-877. The airr package is already a dependency, so we can just just do as Jason said and check against airr::RearrangementSchema['locus'][['enum']]

‌