added option list refactoring
refactored to --method
only refactor at word boundaries
refactored to --method
bugfixes to tests
bugfixes to tests
bugfixes to tests after option refactoring
refactored to --method
refactored to --method
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
command line refactoring
refactoring command line options - batch # 1
refactoring command line options - batch # 2
merged refactoring changes