search

ga4gh / vrs

Extensible specification for representing and uniquely identifying biological sequence variation
https://vrs.ga4gh.org
Apache License 2.0
80 stars 34 forks source link

Rename `sequenceTerminals` to `adjoinedSequences` in the new Adjacency class in 2.0 #456

Closed larrybabb closed 10 months ago

larrybabb commented 11 months ago

During the 12/7/23 SV meeting @d-cameron and the group discussed the new Adjacency class and mentioned the need to rename the sequenceTerminals attribute to provide a clearer term for what was being represented in that attribute. The term connection was offered as a better alternative.

ahwagner commented 11 months ago

I think we discussed 'junction' for this, and that term would be my preference due to it 1) having intuitive semantics as part of an adjacency and 2) aligning with the VICC Fusions and HGVS terminologies.

larrybabb commented 11 months ago

@d-cameron I know on the last call you and I seem to settle on connection but @ahwagner is making the point that junction would be better. I think you were hesitant to go with junction. Can you weigh in on whether junction is acceptable or not? It would be nice to get this closed out asap.

ahwagner commented 10 months ago

I was wrong. I looked back at our notes, we all agreed on adjoinedSequences.

larrybabb commented 10 months ago

@ahwagner Since the adjoinedSequences attribute on Adjacency can be either 1 or 2 sequences, should we drop the plural form of the attribute name? Or go with adjoinment ( or something that represents the notion of one or two end points on one or two sequences that are involved in the Adjacency?

larrybabb commented 10 months ago

@ahwagner new question : Does the linker property of the Adjacency ONLY work if there are 2 adjoinedSequences? Or can you have a linker when there is only 1 adjoinedSequences?

d-cameron commented 10 months ago

Linker works even when you only have one side. Vcf single breakends will contain the (partial) sequence that is connected to the ref and the given location. Typically this occurs when one side cannot be unambiguously placed (e.g. SV into a centromere) or not placed at all (e.g. viral integration against a host-only reference).

On Thu, 4 Jan 2024, 05:48 Larry Babb, @.***> wrote:

@ahwagner https://github.com/ahwagner new question : Does the linker property of the Adjacency ONLY work if there are 2 adjoinedSequences? Or can you have a linker when there is only 1 adjoinedSequences?

— Reply to this email directly, view it on GitHub https://github.com/ga4gh/vrs/issues/456#issuecomment-1875813054, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABOBYOCTPZC6BKUEYZ2RJ4TYMWRYPAVCNFSM6AAAAABALFTNFSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZVHAYTGMBVGQ . You are receiving this because you were mentioned.Message ID: @.***>