filter_vep_transcript_csqs does not work for passing list of CSQ terms

[mike-w-wilson]

There is a bug here:

gnomad_methods/gnomad/utils/vep.py

Line 788 in 0198658

criteria.append(lambda csq: csqs.contains(csq.most_severe_consequence))

The most_severe_consequence field is a top level vep field, at the same level as transcript_consequences, so the way this is currently built does not work as the function looks for most_severe_consequence inside of transcript_consequences here. All other vep fields that get worked on in this function are within transcript_consequences so they work.

[mike-w-wilson]

I missed that

gnomad_methods/gnomad/utils/vep.py

Line 273 in 0198658

def add_most_severe_consequence_to_consequence(

needs to be run first -- should add a note this function wont run without it

[mike-w-wilson]

This was addressed within broadinstitute/gnomad_methods#713