GATKTool.createVCFWriter() for honor the command line parameters. This should be changed the tools that output a VCF.
CommandLineProgramTesterto use instead of our hack of CommandLineProgramTest. We should create or own class changing the methods to fit our code, and make or tests implement that tester.
The current GATK4 framework (https://github.com/broadinstitute/gatk/commit/038703af5ab4e817f1747d73e9ce2c14c2e26f69) include several things that will improve this toolkit:
GATKTool.createVCFWriter()for honor the command line parameters. This should be changed the tools that output a VCF.CommandLineProgramTesterto use instead of our hack ofCommandLineProgramTest. We should create or own class changing the methods to fit our code, and make or tests implement that tester.