Created EpitopeCollection, refactored effects, fix assertion failure while annotating silent stop codon

[iskandr]

Created an EffectCollection, which is used for filtering and grouping sets of effects.
VariantCollection.effects() now returns an EffectCollection.
Merged functionality of top_effect() and highest_priority_effects into EffectCollection.top_priority_effect()
Created a base class Collection from which VariantCollection and EffectCollection get their simpler methods like __iter__ and __len__
Simplified the effect hierarchy, expanded the ambiguous aa_pos (which means slightly different things for different effect types), into the more explicit aa_mutation_start_offset and aa_mutation_end_offset.

Fixes #64 and #58, #63

[arahuja]

Just a list comprehension?

[arahuja]

This looks good to me overall, though prob worth someone else scanning through as well @tavinathanson @timodonnell

Two general things seem odd to me:

1. effect __lt__, sorting the effect by the variant might make sense in some cases, but I'm not sure that is always the expected ordering, especially when effects are usually sorted by some priority?
2. The start_offset on Silent is a bit weird, since it creates a nonsense interval, and the start_offset is inclusive in every case but that.

[iskandr]

@arahuja Do you think the effects should be sorted by priority instead?