airr-community / airr-standards

AIRR Community Data Standards
https://docs.airr-community.org
Creative Commons Attribution 4.0 International
35 stars 23 forks source link

Minor germline style issues #673

Closed javh closed 1 year ago

javh commented 1 year ago
Genotype:
        inference_process:
            type: string
            enum:
                - "genomic_sequencing"
                - "repertoire_sequencing"

Should repertoire_sequencing be split into mRNA and gDNA sequencing?

AllelleDescription:
        inference_type:
            type: string
            enum:
                - "Genomic and rearranged"
                - "Genomic only"
                - "Rearranged only"

Use of spaces and capitals is inconsistent with other germline fields. Should these be snake_case?

javh commented 1 year ago

Second point also applies to RearrangedSequence.observation_type

javh commented 1 year ago

Should GenotypeSet.genotype_class_list be named genotypes instead?

javh commented 1 year ago

Ignore the first, for the second, from #674:

Check for snake_case in all enums. Enforce snake_case instead of requiring quotes around enums, except in cases of currently in-use fields, which will require a version bump to change the enum values (make a ticket for v1.5.0). Require quotes for in-use fields with spaces in enum values.