Merge branch 'master' of github.com:cboursnell/transrate into cboursnell-master

Conflicts:
	lib/transrate/assembly.rb
	lib/transrate/comparative_metrics.rb
add c ext build artefacts to gitignore
bump bindeps dependency version to get bzip2 support
bump bettersam version number
Merge branch 'master' of github.com:Blahah/transrate
Merge branch 'master' of github.com:cboursnell/transrate into cboursnell-master

Conflicts:
	transrate.gemspec
git push origin masterMerge branch 'cboursnell-master'
add OSX build to samtools deps, update linux build link
Merge branch 'master' of github.com:cboursnell/transrate

Conflicts:
	deps/deps.yaml
Merge branch 'cboursnell-master'

Conflicts:
	lib/transrate/assembly.rb
	lib/transrate/comparative_metrics.rb
minor formatting
remove dependency on bio-samtools
fix samtools which command
minimise hash lookups during sam processing
check for existence of files before running samtools commands