new restructuring, new symbolic links to the main classes, the buspecs have moved to the build directory. The executables are removed. All the datafiles are under theone folder including the databases. Now I'm working on the the commandline version so it works again and it works in tandem with the gui output parser.
Changed logic of command line behavior. Now it reads everything in from a textfile called datafiles/options_text and will output those options to a csv or json document. If you want the crap blastout output can still turn off concatenation. But I don't see a good reason to keep that around, I'm checking everything and it seems to work. MP and regular
Merge pull request #10 from jwillis0720/new_build

New build