Remove Fall2012 Specific files

These were added in the fast-forward merge, but really shouldn't be part
of master as they are specific to the Fall2012 Branch.
Measure if Dvir dilutions do the right thing
.SECONDARY preserves intermediates in the Makefile
Add in version numbers to allow easy updates
Add in the Virilis reference genome and annotations
Remove LowVolume specific files
Filter ribosomal/smallRNA orthologs from the Dvir annotations
Enhancements to MakeSummaryTable

Allow more flexibility on sub-directories, filenames

Allow comment characters in RunConfig

Allow gene names like nan by interpreting the key as a string, not as
whatever pandas defaults to.
Add in MakeSummaryTable generic changes from LowVolume
Merge branch 'master' of github.com:petercombs/EisenLab-Code
Add in code to make combined melvir datatables
Remove long-broken commented out lines
Script to analyze how consistent the Mel is

Compares between different mel samples. Takes the geometric mean of the
fold changes between samples.
AnalyzeFoldChng takes input file from command line

Seems more flexible that way.
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 option for missing values to be zero