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Pre release 94 cleanup

Marek Szuba requested to merge github/fork/at7/pre_release_94_cleanup into master

Created by: at7

Requirements

Functionality which is removed from core API is stable and contained in variation API.

Description

This is part of our effort to remove variation dependencies from the core API. I removed all deprecated code that is not used in the web code and compara API. I cannot remove Bio::EnsEMBL::Slice::get_all_VariationFeatures() because in the web code this is called on modules/Bio/EnsEMBL/Compara/AlignSlice/Slice.pm. Not sure if there is a way around this. However, get_all_somatic_VariationFeatures, get_all_somatic_VariationFeatures_by_source, get_all_somatic_VariationFeatures_with_phenotype and get_all_VariationFeatures_by_Population are called on proper core Slice objects in the web code. I will replace those for release/95 which gives me enough time for testing. get_by_strain will be removed in release/95 together with code that still uses get_by_strain at the moment.

Use case

Code allows to get variation data on slice objects.

Benefits

remove variation code from core API and therefore reduce possible ways of getting variation data for a slice. Remove code duplications.

Possible Drawbacks

Possible that I have overseen dependencies which could result in broken web views. But enough testing should prevent that.

Testing

Lot's of manual testing of web views which use the code.

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