Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

Feature fix missing values

Fix for wrong messages when config value does not exist

Now also fix for #112

See merge request !89

Make a val for globalConfig, test should now be able to override it so unit test are not depending on a global var