collect effect annotation errors in dictionary, only look up overlapping...

[iskandr]

... transcripts and construct the Gene objects later

[tavinathanson]

Should raise_on_error be in the VariantAnnotator constructor instead of peppered across different methods?

[iskandr]

The most common use case is VariantCollection which uses VariantAnnotator under the hood. Not sure how to economize on raise_on_error since you'll need one arg in VariantCollection and another in VariantAnnotator.

[tavinathanson]

Yeah, I figured VariantCollection would pass it through to VariantAnnotator. The constructor just felt more appropriate to me, based on knowing far less about the code than you do.

[iskandr]

The constructor feels a little clumsier to me since the typical usecase seems to be:

1. Construct variant_collection = VariantCollection(some_vcf_path)
2. Call variant_collection.variant_effects()
3. Encounter an error
4. Decide the error is irrelevant
5. Call variant_collection.variant_effects(raise_on_error=False) to ignore the error

Having to create a new VariantCollection seems like a very minor hassle but it also doesn't have a clear payoff.

[tavinathanson]

👍

[tavinathanson]

A few comments, but generally looks good to me!