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ga4gh / vrs

Extensible specification for representing and uniquely identifying biological sequence variation
https://vrs.ga4gh.org
Apache License 2.0
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Epic #480 "Create Adjacency" #488

Closed ahwagner closed 7 months ago

ahwagner commented 7 months ago

addresses #480 "Create Adjacency" related to #429

Mrinal-Thomas-Epic commented 7 months ago

Don't we still need the homology flag to distinguish between imprecision due to assay limitations vs equivalence of sequences on either side of the adjacency?

ahwagner commented 7 months ago

I don't know; do we? The homology flag was removed a while ago, so I don't remember why exactly that change was made. I understand the two scenarios you are describing, but is this distinction important? I haven't explored this deeply, but it seems to me that you can infer when each of these situations are taking place from the sequence content; and if you cannot infer it, that it doesn't make a difference. Maybe a good conversation topic for Connect.

For now, I will add it back in as an optional property, and will open #489 for discussion and use cases on this topic.