runExpression.py - added ttest
Masker.py - fixed: segmasker now does softmasking
tests - fixed tests for modules
pep8 - various minor refactorings
Merge branch 'master' of ssh://github.com/CGATOxford/cgat
pep8 - various minor refactorings
merged with Andreas changes
Merge branch 'master' of ssh://github.com/CGATOxford/cgat
gtf2gtf.py - mark duplicates uses GTF iterator
pep8 - various minor refactorings