Make CMAKE the default build script

* use add_compile_options instead of hardcode setting of the env variable
* remove lib from include directories
* add header files to the source list
* include htslib directories at the cmake build location (no longer using the git-submodule)
* remove git submodule and use htslib via cmake from now on.
* exclude tests from building by default
* build release by default, but tests in debug mode
* remove boost build files
* add cmake to travis
* add release / debug options to the build
* add run_test option for building and running tests in one command