[ ] Move the command-line scripts are located in a cli directory, from script.
[ ] Move nappy/utils/compare_na.py to cli/ - but remember that compare is imported in tests and other code, so the underlying functions need to remain in a library rather than a script.
[ ] Maybe compare_na.py and compare.py are the same!?
compare
is imported in tests and other code, so the underlying functions need to remain in a library rather than a script.