moved from the old argparse to doctopt

much more pleasant than argparse or the standard library's
optparse.
added validation to make_index.py and rewired the commandline to

the actual function call
forgot to add validators.py in previous commit
bug fixes and improved histogram in make_index
added validation to align.py and rewired command line parsing

to work with the docopt option names.
bug fixes to align.py

* ensured that code will work for 4cutter/4cutter 4C assays
* renamed variable to reflect order of digestion rather tan 6cutter/4cutter
  distinction
* bug fixes
added validation of command line for fragcount.py

and hooked up new arguments to processing functions
adding command line validation to bin.py

and hooking up new options to processing functions
finished plumbing in docopt and validation

also many small bugfixes.  This should be
revision with all parts working correctly.
Merge branch 'docopt' into develop
added documentation
added detection of "blank" fragments

these are fragments that don't harbor a secondary RE site.  fragment
output now contains another column that indicates the distance between
the left and the right primary RE sites (or -1,-1 if there is no
secondary site; ND if it was not tested).
bug fixes (e.g. division by null length for N frequency)
modified the criterion for excluding short fragments

instead of 2 * flank_len it's not flank_len + 10.
Merge branch 'blind' into develop
allow existing output directory
fixed is_dir validator bug
fixed a bug that caused fragcount to fail if genome name contains underscores

now ignores any underscores in the genome name
another bug with underscores fixed
Merge branch 'fragcount' into develop