Added automatic output of ROVER input-file

ROVER project —> https://github.com/bjpop/rover
Created --roverfile parameter and fixed output bug

BUG: Rover output file not cleared at beginning of each run of script.

SOLUTION: Created parameter for roverfile output, moving file creation
out of the print_best_primers function (which was called multiple times
during a single run, resetting the file OR appending incorrectly
depending on the file open argument) into the parameters.

Parameters are called only once, facilitating correct behaviour.
Fixed gitignore extra entry for chromosomes directory