Closed williamdlees closed 1 year ago
Now has the two items agreed at our last meeting for implementation in this release:
fixed UndocumentedAllele name
Withdrawn while I work on updating the test data
From the call:
species
, mhc_class
, and observation_type
as essential makes sense.RearrangedSequence.derivation
.coding_sequence.description
can we be more explicit here? Can we use the following as a guide? https://docs.airr-community.org/en/stable/miairr/specification_miairr_ncbi.html.Genotype.receptor_genotype_set_id
in a minor release. Maybe v1.5.MHCGenotype.mhc_alleles
) with reference should be fine for v1.4.2.Good to merge in after the above fixes.
species
, mhc_class
, and observation_type
marked as essential.RearrangedSequence.derivation
(the name waa reviewed and agreed by IARC some years ago). Possible alternatives should they be required could be derived_from
, sample_source
, nucleic_acid_class.
.coding_sequence.description
changed to nucleotide sequence of the core coding region, i.e. the coding region of a D-, J- or C- gene, or the coding region of a V-gene excluding the leader
. I think this is pretty specific now.Re-structuring of MHCGenotype and Genotype objects to include object references rather than embedded objects looks like it is correct to me.
From the call:
AlleleDescription.allele_similarity_cluster*
in the Germline documentation (see above comment from @bussec).
In germline objects, remove all nullable: false entries and add x-airr: qualifiers instead.