Masai replaced with Yara
Merge branch 'masai_fseq' of github.com:clark-lab/ngsane into masai_fseq
compatibility with external bams improved and smoketests updated
Merge branch 'masai_fseq' into rnaseq

Conflicts:
	bin/trigger.sh
	mods/cufflinks.sh
	mods/cuffnorm.sh
	mods/cuffquant.sh