OK, looked at the source and the only properties that forward through the alternate effect are mutant_protein_sequence, modifies_protein_sequence, modifies_coding_sequence
So, you have to currently explicitly check, which seems like a recipe for making this mistake often
Possible solutions: add a is_substitution method or change how exonic splice sites are handled
One possible alternative would be just having every Intragenic effect take a splice_site boolean attribute
Or something else that better preserves the meaning of the class hierarchy
From @tavinathanson:
yikes glad we caught it now at least
how about we invert the meaning of alternate_effect and have every effect have an optional alternate where ExonicSpliceSite would be one such alternate?
similar to splice_site boolean, which also seems fine to me
i think either of those is better than is_subsitution which feels like a hack
for now i'm going to hack around this in cohorts until we know exactly what we want in varcode
From @tavinathanson:
From @iskandr:
From @tavinathanson: