comment corrected
examples adjusted
Bugfix dummy file generation
merge with master
Added option to only use uniquely mapped reads.

HTSEQCOUNT_UNIQUE unique added.
Added R sessionInfo() output to R scripts.

Added to all R scripts in tools:

sink(type = "message")
sessionInfo()
Added list of required packages from R scripts.
Bugfix checkpoint recovery
cleanup trinity duplicate definition
new mod tempate file added
Merge branch 'master' of github.com:clark-lab/ngsane
merge with master