Test infrastructure for framework users

[magicDGS]

I'm using GATK4 as a framework to implement my own tools, and it will be nice to have a way of perform integration tests using IntegrationTestSpec. Nevertheless, it requires the extension of the CommandLineProgramTest to run the command, and thus it is extending BaseTest.

The issues that this infrastructure generates when trying to use this test classes are the following:

• BaseTest loading of GenomeLocParser is annotated with @BeforeClass, which throws an error because the reference genome (hg19MiniReference) is not present in the repository.
• CommandLineProgramTest is using org.broadinstitute.hellbender.Main for running the commands, but for custom tools the instanceMain with a different list of packages. Although this could be solved by extending the class by another abstract class.

I propose (and I can implemented if you agree) the following:

• CommandLineProgramTest not implementing BaseTest.
• CommandLineProgramTest as a real abstract class without implementations of getTestDataDir() or runCommandLine()
• Abstract GATKCommandLineProgramTest extending both CommandLineProgramTest and BaseTest, sited in org.broadinstitute.hellbender.utils.test and used in all integrations tests in this repository and the protected repository.

[magicDGS]

Related with #2125