Define transcript preference

[holtgrewe]

Is your feature request related to a problem? Please describe. In the case that both ENSEMBL and RefSeq sources have MANE transcripts, there is no rule which one to prefer.

Describe the solution you'd like Allow users to select a preference, defaulting to RefSeq.

Describe alternatives you've considered N/A

Additional context N/A

[tedil]

Right now, there's only --transcript-source to restrict to ensembl, refseq or both. But the point of this proposal is that in the case of both, have a priority of one over the other? I.e. something akin to --transcript-source-priority refseq,ensembl? Does that play nice with other transcript picking options that we have?

[tedil]

Closing this, feel free to re-open if you feel this is still relevant/needed!