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
added in compseq error message if its not installed
added error message if genome fasta file isn't present, motif finding will not be performed.
added back in homer location for motif printing