Revert "Added modifcations to handle fixes for rendering vcf."

This reverts commit 37dbade4ee34d3dbba1fc6dbe82fa86ba8151899.
Merge branch 'release-1.2' into issue-192-gencode-vcf-rendering

Conflicts:
	oncotator/output/OutputDataManager.py
	test/testdata/maflite/example.normal_sample_name.maf
	test/testdata/vcf/maf2vcf.example.normal_tumor_sample_name.vcf
Removed deepcopy call which should greatly speed up the file-based cache.