Begin supporting GRCh38

This PR is the start of moving this repo to support GRCh38.

Major changes:

Updated process_context_ht and removed process_vep to reflect updated inputs for GRCh38 and updated utility functions in gnomad_methods repo (rmc/utils/generic.py)

Minor changes:

Removed all references to v2 flagship LoF resources (no longer needed; rmc/resources/gnomad.py)
Bumped GENCODE and VEP versions; also converted TableResources to VersionedTableResources (with TODOs; rmc/resources/reference_data.py)
Updated default reference and gnomAD versions (rmc/resources/resource_utils.py)
Updated freezes and removed references to obsolete ExAC resources (rmc/resources/rmc.py)
Removed obsolete ExAC functions (rmc/utils/generic.py)
Updated liftover options for de novo reference data (rmc/utils/generic.py)
[NEW] Fixed pylint errors associated with process_context_ht call in rmc/utils/missense_badness.py

broadinstitute / regional_missense_constraint