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

Populate max_length in meta_coord table now.  Additionally, meta coord is automatically populated now and no longer needs hardcoding for each species.

Initial version of program to convert short introns into frameshifts.  Currently cannot handle all cases and needs some significant reworking.