change in setup.  Took out a pdb.set_trace()
Script location
 oops I put them in bin previously and wanted to put them into scripts/
Adding scripts
Updating readme
Fixed some small bugs.  Updated copyright.  Adjusted some annoying coding habits.
Added a function to input.py that takes an "EMMA" formatted covariate file where the rows are covariates and the cols are individuals.  Added an option to the GWAS script to take this as input instead of the plink formatted covariate file.
Small but in gwas script and some cleanup.
Moved README to markdown
moved readme