Major refactoring of the library to be more package oriented design

[ypriverol]

@husensofteng I will refactor the structure of the github project to be more like a python package. My proposal is the following:

• github root
  • pypgatk
    • pypgatk.py
    • .. all packages
    • config/
    • testdata
    • tests
  • requirements.txt
  • setup.py
  • LICENSE
  • READMED

[ypriverol]

This has been done