increase version requirement for bam-read
make sure that stuff isn't run if it doesn't need to be
add timestamp to logger #94
print help message when run with no arguments #93
missing dependencies are now printed with their version number
Merge branch 'master' of github.com:cboursnell/transrate into cboursnell-master

Conflicts:
	deps/deps.yaml
	lib/transrate/read_metrics.rb
Merge branch 'cboursnell-master'
update coverage calculation, fix tests
round coverage to 2dp