feat(l2g): implement variant consequence features from VEP

[ireneisdoomed]

✨ Context

Closes opentargets/issues#3554

🛠 What does this PR implement

• Removes the dependency of the consequence to score file. This is now an attribute of the VariantIndex class
• Implements the features described in Implement variant consequence features from VEP into L2G issues#3554 following the formulas defined in https://docs.google.com/spreadsheets/d/1wUs1AprRCCGItZmgDhc1fF5BtwCSosdzFv4NQ8V6Dtg/edit?gid=452826388#gid=452826388
• The approach is tested with semantic tests

🙈 Missing

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[addramir]

Why do we still have L2GGoldStandard? Isn't it going to be removed?

[ireneisdoomed]

As agreed offline, we'll do that once we tackle opentargets/issues#3525

[addramir]

How do we assign the genes for this studyLocusId?

[ireneisdoomed]

Genes come from VEP. It's the genes of the transcript that the variant overlaps with in a 500kb window

[addramir]

For variantId - yes, but we have many varintIds in one studyLocusId. So just to be sure - we use the union across al varaintIds? And if varintId is not assigned to geneId we assume its VEP score is 0?

[ireneisdoomed]

@addramir As discussed, the maximum score is fetched from the variant index directly. This branch now has #811 as a base. I'd suggest merging that one first.

[addramir]

Approved