New file to facilitate installation into $HOME/bin
Fixed bug where pair_id was not being incremented during output, leading to reads all having the same name
Added documentation for install2home.sh
New file.  This script will create OGE jobs for faster pipeline execution
Initial coding up thru "bwa sampe" complete
Added merge and readname-sorting steps
Added variable GEGENERIC so that users can customize all the scripts with "module loads" or whatnot that their system may need