Make denoise_wrapper work again after using the fancy existing_filepaths option parser, which broke the code.
Use 'existing_filepaths' option in denoiser.py
added code and test to extract sample ids associated with state changes in an individual

to support pre/post (or paired difference) tests
updated test function name
updated to filter out individuals that don't have data at all states
added function to extract mapping file metadata category associated with different states
added test cases
more extensive tests and a bug fix
more extensive tests
ugly, but first working version of the script
cleaned up output plots
fixed bug in handling of plots with only one row of subplots
deleted out-dated example output
improved plot output and updated example output
fixed issue with placement of labels
updated header information
added error check
simplication of code
more code clean-ups and added bonferroni correction to stats output
added bonferroni correction to example output