this code/ directory contains a lot of scripts that are called at various stages in the analysis pipeline. Some are probably not actually called but I have not sorted them out yet.  Many old or irrelevant pieces of code have been moved to the code/old_unused/ directory to reduce clutter.  Other scripts have been moved to the code/figure_scripts/ directory if they are not explicitly called in the pipeline but are useful for making some figures.  

code/driver_scripts/ contains the main pieces of code that are run to actually
carry out the analysis, which in turn call many pieces of code in code/.

-MAX 2015
