fixed pysam version to 0.7 in setup.py.
Added error handling for contigs present in bam files but not in contig
file. Separated error handling into a new module.
Adding module for handling errors.
updated docs
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
changed version number
Fixed informative plots. added flag -plots. Added separate module for
plotting.
fixed bug in score function. 
Fixed separate module for plots
Fixed flag '-plots' for plotting option
Cleaned up code.
Merge branch 'feature/print_stats' into develop
added module plots
fixed version
Merge branch 'feature/updates' into develop
Added parameter --iter for number of iterations in BFS.
Changed dispersity score of links.
Fixed bug in plotting.
* Fixed bug in dispersity score (a KS test from scipy)
* No decision of path is made if scores are similar (breaks paths)
* Added dotplots of number of links to dispersity score for
verification. 
* BESST now has dependency of scipy. Added this to setup script
small gap fix - Francesco
Fixed bug in removing 0 score edges i G_prime. Now all edges in G are
also removed in G_prime when searching for paths. This is an important
fix.
setup.py merged