release candidate 2
Merge branch 'master' of github.com:clark-lab/ngsane
support htseqcount on cuffmerge gtf in pipeline
Merge branch 'master' of github.com:clark-lab/ngsane
Bugfix
Merge branch 'master' of github.com:clark-lab/ngsane
Compatibility with samtools v1.x improved
Merge branch 'master' into rnaseq

Conflicts:
	mods/_run.d/TOPHATCUFFHTSEQ
	sampleConfigs/pipeline_RNAseq.txt