Created by: magaliruffier
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One or more sentences describing in detail the proposed changes.
The proposed change updates the list of sources known to be attached to genes, so we are not missing data for some species.
Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place.
In the xref pipeline, there is a step to copy xrefs from the genes on the primary assembly to those on the alternative sequences. This uses a hard-coded list of xref sources which are allowed on gene level. It did not contain MGI, so names were not copied to alts in mouse. The list has now been updated to include all the known gene sources across all vertebrate species. This was spotted by a user who was wondering why alt alleles did not have the same gene symbol as their reference on the primary assembly, unlike human where it is done correctly. An example can be seen here: http://e92.ensembl.org/Mus_musculus/Gene/Alleles?db=core;g=ENSMUSG00000116203;r=CHR_MG3686_PATCH:111254283-111404050
If applicable, describe the advantages the changes will have.
Mouse genes on alternative sequences will have the same name as their alt allele on the primary assembly.
If applicable, describe any possible undesirable consequence of the changes.
Gene names for the mouse annotation will change.
Have you added/modified unit tests to test the changes?
There is unfortunately no test suite for the xref code, but the code compiles and was run on sample data.
If so, do the tests pass/fail?
The whole pipeline was run on the latest mouse database and fixed the example reported by the user.
Have you run the entire test suite and no regression was detected?
Yes, although the test suite does not test this particular area of the code.