Created by: magaliruffier
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Using one or more sentences, describe in detail the proposed changes. Massive cleanup of the xref configuration file. Deprecated sources have been removed, so have duplicated sources (no species-specific RefSeq sources but everything from the same file). Configuration for all vertebrate species has been removed as they inherit directly from the vertebrates configuration, only species-specific (HGNC, MGI...) configuration remains. Unfortunately, git does not understand large removal of lines, so it looks like more has been removed than is actually the case
Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. The current configuration file is hard to maintain. It is also not clear what needs to be added where when sources or species get added. This is the first attempt at removing some of the clutter.
If applicable, describe the advantages the changes will have. The file has been simplified, hopefully making it easier to maintain in the future.
If applicable, describe any possible undesirable consequence of the changes. The history will be difficult to disentangle as git does not like removing a large number of lines
Have you added/modified unit tests to test the changes? The pipeline was run on all vertebrate species with the complete set of changes. Results were compared with those from a previous run to ensure all sources are still correctly added for all species.
If so, do the tests pass/fail? The results are comparable to previous run.
Have you run the entire test suite and no regression was detected? xref_config2sql.pl runs without errors