GitLab

much code duplication removed by adding load_adaptors which other load methods call. load_adaptors is now also called if an unknown DBAdaptor is passed (which could happen with registry autoloading. Added a test for variation adaptor

Laura detected subtle repeat_masked sequence bug. On reverse strand sequence, masking happened after reverse complementing, putting it into wrong spot

all objs_from_sth have a small buglet, fixed for this one. Features overhanging the slice and not overlapping were not filtered out

Added get_available_adaptors to get the pairs of name / adaptor modules. This should make it easier to read etc

Added $subname in the key of the DEPRECATED hash. Useful when calling several methods from the same line like when using the Bio::EnsEMBL::Test::TestUtils::test_getter_setter method.

Entire diagnostic execute function should be commented out.  Statement execution slightly slower otherwise.

more indexes on align feature tables so range queries are still quick when no logic name is provided