Improved consistency in GTF.py
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
development of pipeline_exome_cancer and modification of class Bismark in PipelineMapping
added option list refactoring
resolved conflicts
refactored to --method
added documentation for bed2fasta, gff2gff, gff2psl
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
gff2fasta.py documentation
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
gff2stats.py docs
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
command line refactoring