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.
Merge pull request #6 from Kiwwa/heelseqdev

Heel Sequence Addition
Fixed gitignore extra entry for chromosomes directory
Merge branch 'runautopep8'
Renamed chr variable to chromosome

chr is a reserved variable in python (for a character variable type).
Replaced unneccesary quotation-marks and seperated lines > 79 characters

After running PyLint over Primer_design.py, cleaned formatting issues
that were found.
Ran autopep8 after previous cleanup
Merge branch 'runpylint' of https://github.com/Kiwwa/hiplex-primer into runpylint

Conflicts:
	Primer_design.py