Removed compiled files from version control, and added make file
renamed make.sh and added 2 new scripts
added mit x11 license to everything
Merge remote-tracking branch 'upstream/master'
bamliquidator now has 0 main return code on success
Changed bamliquidator_make.sh to makefile, so now it can be be built with just the make command.  I also removed the redundant warning gcc flags (-Wall stands for warn all, and I confirmed that -Wall included all the other warnings).
Inserting counts
Added an error check in the liquidator, and kicking off overnight run
Added some comments
Fixed bug
Added optional checking against baseline
Added optional checking against a baseline
bug fixes: no longer double counting boundaries, and skipping irelevant chromosomes
Getting ready to run on tod
Merge branch 'master' of github.com:jdimatteo/pipeline