Add option handling and --version option.

Added changes entry. Added test for application to give correct output
with —version flag. (failing). Added subroutine parseBamCli to do
option parsing, stubbing in placeholders for defaults and config file
options, Added —version flag option and anonymous sub to parse it. All
tests pass, 100% coverage. Manual run of installed program gives
expected version output. Update read me
Merge branch 'basic-option-handling'