Debugged

Arthur's new version.

Fixed duplicated breakpoints. 
Fixed cleaning up of temporary files.
Fixed exception handling. 
Fixed single-end data bugs.

Updated the driver script: 
1. got rid of intermediate shell driver script and is fully Pythonic. 
2. JVM memory is as script option and performs a rough required memory check.
3. changes to subprocess calls that should take care of potential blocking of script.