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Task variation/remove deprecation status

Marek Szuba requested to merge github/fork/at7/task_variation/remove_deprecation_status into master

Created by: at7

We cannot remove those methods from the core API. The webcode API depends on them. They are used for example here: https://github.com/Ensembl/ensembl-webcode/blob/release/98/modules/EnsEMBL/Web/Query/GlyphSet/Variation.pm#L205-L209 And here https://github.com/Ensembl/ensembl-webcode/commits/release/98/modules/EnsEMBL/Web/Component/TextSequence.pm The slice used in the webcode is a compara AlignSlice. If I rewrite the method to be used in the VariationFeatureAdaptor and pass the AlignSlice from the webcode the method doesn't work.

Dan S commented a while ago saying: I'm having to revert that because it doesn't seem to interact well with AlignSlices (rather than real Slices). This breaks variant display on the Phylogenetic Context page (focus variant and other variants do not display). It looks like this is because the new method (in the VariationFeatureAdaptor) eventually calls get_and_filter_Slice_projections in Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor inside the core code, which objects that the slice has no adaptor available via ->adaptor.

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