Refactoring all of the scala scripts to centralize everything related to the bamtypes file.
--Creating a shared BamTypes.scala
----moving reading and writing to the bamtypes file
----moving AnnotatedFile and Abrv file into BamTypes.scala
----renaming AnnotatedFile to AnnotatedBamFile and AbrvFile to NamedFile
Moving BamTypes code into a better location and adding it to the build script.
--We shouldn't have to add -S BamTypes.scala to runs now.