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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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Need "start" position in RLE #436

Closed larrybabb closed 10 months ago

larrybabb commented 1 year ago

https://github.com/ga4gh/vrs/blob/c693ac3e8ac85d793a7fe73529504038aa71c815/schema/vrs-source.yaml#L480

Without the start position of the RLE in an allele's state attribute we would not have a fully defined allele. The start position is definitional IMO.

Please explain otherwise.

ahwagner commented 10 months ago

An RLE appears in the context of an Allele, as does an LSE or an LE. In each case, these expressions are all evaluated in the context of the containing Allele. So, the start and end for the RLE are found in the parent Allele object. This is different from the DerivedSequenceExpression, which let you express any reference sequence regardless of context.

Closing for now, please re-open with an example if this is unclear.