Added new script, add_categories.py
	modified:   add_categories.py
Added script and modified it to use command line arguments with argparse
	modified:   calc_shared_allele_fracs.py
changed to use command line arguments with argparse
added new script calculate_pis.py to calculate nucleotide diversities, added a small test file 9/25/2014, small changes
	modified:   calculate_pis.py

Added checks for divide by zero and uncommented part that looks up length of reference sequence
	new file:   run_mosaik.py
	new file:   bam_file_processing.py
Script to call bam processing steps added
	modified:   run_mosaik.py
Added argument parsing