Use Nucleus' protos instead of VcfHeader

[arostamianfar]

Nucleus VcfHeader protos are much nicer to work with than our VcfHeader class. We should update the code to use the protos. Need to first resolve #420.

Important note: we should make sure that there are no performance penalties when switching to use protos as protos are known to be less performant than native python objects. Given that we use headers mostly during initialization, then it likely won't have a noticeable effect. The only exception is in the ProcessedVariant class when checking for Number=A and some annotation fields. Proto lookups can be avoided by just creating an auxiliary map ({key, number}) inside that class.