Creates the reference object

Will allow to access to the reference databases stored in the DB.
Required for processing pipeline.
This PR also fixes a bug on test_setup.py. It was not testing anything, as now the cal to check_count does not raise anything. I had to fix anything related with this issue.
It changes the DB. The reference table now points to the filepath table to store the reference files
Because I cannot repeat the same column name 3 times... And i need 3 ids: sequence, taxa and tree.