started development of changing argument parser from optparse
to argparse.
Started change to argparse from optparse. Things to to:
1 Fix mutually exclusive arguments
2 throw error when too few/many ars are given.
3 Error handling in general.
Updated to argparse as argument parser. using pysam 0.7 instead of pysam
0.6.
Merge branch 'feature/argparse' into develop