Updated GPL16043.sh to use scripts in current directory
Removed compiled files from version control, and added make file
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
Updated make file to work on tod
table names now all lowercase
Added error logging
Updated counter to process next file in a directory
Corrected syntax errors
Enhanced error reporting