Added modifcations to handle fixes for rendering vcf.
Updated determining the is split logic.
Differentiate between num = . and num >= 0 for splitting.
Three maf2vcf conversion tests still failing.
Corrected unit test ground truth.
Adjusted a unit test to check info field correctness.  Minor code cleanup.
Minor code cleanup.
Corrected the additional parameter that was extraneous.  Some code cleanup.
Fixed ground truth that was causing erroneous failures.  One failing unit test left.
First cut at fix for improper GT rendering.  All unit tests may be fixed.
Cleanup of code.  Including removing tmp file proliferation.
Fixing int vs. str issue.
Fixing int vs. str issue, again.
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.
Merge pull request #200 from broadinstitute/issue-192-gencode-vcf-rendering

Issue 192 gencode vcf rendering