Merge pull request #35 from ICGC-TCGA-PanCancer/master

sync master to dev
Fixed annoyance for those working with cross platform perl installs
command arg not documentes
Clean up version inheritance and add test to check all objects import it
Update to handle bugfix in biobambam
Merge pull request #38 from ICGC-TCGA-PanCancer/dev

merge updates for bugfix in biobambam