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Missing translation end data for variants

Marek Szuba requested to merge github/fork/ens-lgil/feature/overlap_translation_tv_master into master

Created by: ens-lgil

Description

Spotted that the end data returned by the overlap/translation for the type transcript_variation was wrong: the start = end is only true for SNP, but this not the case for short deletion (spread onto more than 1 amino acid). I believe this is a very old bug (5 years!).

Use case

Example for rs1326874757 (CACCGTCAT/-), it's mapped coordinates on ENSP00000465759 are 995-997 but on REST, the coordinates are 995-995: http://rest.ensembl.org/overlap/translation/ENSP00000465759?feature=transcript_variation;content-type=application/json

Benefits

The REST endpoint will returns the correct coordinates

Testing

Added a unit test in t/overlap.t (required to update the variation test DB)

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