Changes to get Makefile to run properly for DmelDvir data
Configure now uses argparse, can take seqdir

Argparse is more general than trying to parse out the argv, and to show
that, I now add in an optional seqdir argument for dealing with the
default sequence directory (at this moment, useful for the dry-run
purposes)
Fix error where I was accidentally dropping everything
Bug fixes and Plotting refinements

I had not yet ever run either of the two Analyze scripts, and so there
were some things that just didn't work.  Also, the plots weren't totally
clear, so looking at what needed to be changed was instructive, but
nothing totally earthshattering.
Make sure makefile generates all directories needed

Before, the Reference directory wasn't getting created.  I should
probably also do something for prereqs, but another day.
Add in a script to subsample all to same depth
Effectively just fix typos.

Biggest change is in configure, which changes how I deal with globbing
readfiles, since the sequencing center gave them to me in a different
format this time.  Boo.
Make the analysis scripts work better
Handle the subset reads in Analyze*.py
Parallelize CheckCoverage
Check coverage on mel+vir, mel, and vir