Merge pull request #8 from kellrott/dev_cwilks1

Dev cwilks1
Adding stage selection to simplechain
Merge branch 'master' of github.com:kellrott/tcga_realign
Making simplechain work against a single request
Merge branch 'master' of github.com:kellrott/tcga_realign

Conflicts:
	simplechain.py
Fixing readgroup file naming and some timing output
Working on bugs
Merge pull request #9 from kellrott/dev_cwilks1

renamed cgsubmit to cgsubmit_fixed so it would be found instead of the i...
Returning values in submission stage to fix exeception
hopefully fixed pathing/naming issue with bam_merge timing, also cgsubmit_fixed should make a different directory for each run