GitLab

updated biotype functionality to mimic legacy behaviour of setting through biotype() and defaulting to 'protein_coding'

- Added tests to cover UTR-coding sequence boundary for forward and reverse strands

Set an object's default version to 1 when it is created, rather than when it is stored, to allow undef versions (which can then be stored as NULLs in the database).

Check that an analysis exists before calling logic_name on it, needed for testing where a full object might not exist. And just good sanity.

- Fix how UTRs are created, they should be created with start/end relative to the feature, not in genomic coordinates
- Update tests to check UTRs are created correctly when transcripts are fetched from a Slice
- UTR test cases for forward and reverse strand transcripts

This reverts commit 3e24194c.

Fix for ENSCORESW-1816, bioperl's inconsistent handling of incomplete codons across versions. Trim any partial codons when translating unless told not to.

stable_id_version setter/getter for core object types, sets stable_id with a . delimited version or fetches stable_id with .version concatonated (if version is set)