Fix bug when lane trimming is skipped.
Merge pull request #164 from porterjamesj/trim-fix

Fix bug when lane trimming is skipped, thanks to @porterjamesj.
Substitute qualimap QC run with bamtools stats. Provide a more lightweight approach until we can decrease qualimap run times
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Finalization of cn.mops implementation for CNV calling: create BED file with copy number reports and split results by batch samples