Those who follows code development may have noticed creation of another branch, 'consolidate'. This branch contains reorganized structure of code files, allowing to have GUI and command line version within one project. Thanks, Cory. This convenience comes at the cost of manually disabling one or the other group of files for compiling one or the other version. Also, when compiling into command line version, application type should be set to 'Console application'. And it whould be 'Windows Forms Application', when compiled to GIU. Details are in 'BUILD' file.
This restructuring was also aimed in simplifying compilation of Linux version of GenomeRunner. It's on the way, check back soon!
Anonymous