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
Kath deleting pipeline.ini from exome pipeline build directory as this has been replaced with exome.ini
Kath making exome pipeline trackers compliant with pep8
changes for pep8 compliance
Merge branch 'master' of github.com:CGATOxford/cgat
pep8 - various minor refactorings
merged with Andreas changes
fixed syntax error in gtf2gtf.py
Merge branch 'master' of ssh://github.com/CGATOxford/cgat
gtf2gtf.py - mark duplicates uses GTF iterator
pep8 - various minor refactorings
Added a check for spaces into attribute processing for GTF.py. Now first word is assumed to be key, and all others values. Might cause problems if key has spaces, but this wouldn't have work before either.
Merge with master - merge conflicts with GTF.py resolved
merge with conflict resolution for Expression.py