Refactored variant_filter.py.
Refactored variant_filter.py.

Split up some functions and reduced nested if-elses.

churchlab/millstone,churchlab/millstone,woodymit/millstone_accidental_source,woodymit/millstone,woodymit/millstone,woodymit/millstone_accidental_source,woodymit/millstone,churchlab/millstone,churchlab/millstone,woodymit/millstone,woodymit/millstone_accidental_source,woodymit/millstone_accidental_source