decoupled viz from analyze, turned vis functions into objects
updated clip analysis and display to work better
removed bed12 check
did stuffs
fixed processing issue where introns were sometimes ignored during processing.  There are still uncatagorized peaks, but these peaks are now in non-coding genes
fixed issue with clip analysis refactor where regions weren't being saved properly.
updated hg19 genic regions to debugged version of get genomic regions, mm9 still broken
removed idx file that shouldn't have been there
removed re-assign option
Made it so clipper fails gracefully upon lack of input files
get genomic features no longer needs a gff file to run if previous results are cashed.
converted clustering to work with htseq instead of bw files (reduced number of params needed)
refactored count_total_reads to use HTSeq, also made code slightly more pep8 compliant

refactored count_reads_per_cluster to also use HTSeq
removed bigwig files from args, and did massive re-factoring to account for that.  Also Made AS_structure and other args optional, again massive refactoring.
refactored get_peak_locations, split distribution generation and peak location calculation into two different functions.
fixed error message for rna position to make me less worried about errors
fixed small startup bug where argunment names were wrong.
fixed bug where genomic content wouldn't print
removed unnessessary or confusing argunments from script
fixed bug where piechart colors would appear to be off