Integrated util.vcfParser.VCFParser by swapping out util.VCFLineParser.
Deprecated util.VCFLineParser by renaming to util.VCFLineParser_OLD.
Debugging Variant Pool.
Testing VCFParser.
Deprecate VCFLineParser.
Debug strip initial matching bases in VCFParser.
New working template
Merge branch 'master' of https://github.com/ARUP-NGS/Pipeline into DanielBranch
Merge branch 'vcfparser' with the 'master' branch now that VCFParser has been tested.
Merge branch 'master' of https://github.com/ARUP-NGS/Pipeline
Merge branch 'master' of https://github.com/ARUP-NGS/Pipeline into DanielBranch
Rewritten BAM record counter, moved a method from OncologyUtils to Operator.