RescueAmbiguous now works on any species

Thanks to Steven Kuntz!
Merge branch 'master' into Fall2012
Added some old files

CalculateAbundancesStrict is a lightly modified version of
CalculateAbundances that uses the correct "strict" files.

KillAmbiguous is like AssignReads, but different. How? Magic.
Makefile and configure script now honor genome

In the past, I just mapped everything to yeast, but this is really much
better.  I think I caught everywhere it matters.

I had to stop using samtools reheader to fix the header, since I
couldn't know that the chromosomes would be in the same order (and, for
the flies, they aren't)
Allow a ? direction in RunConfig
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.
Remove LowVolume specific files
Add in MakeSummaryTable generic changes from LowVolume
Merge branch 'master' of github.com:petercombs/EisenLab-Code
Add option for missing values to be zero
Code to make a table of ISH images

I made this more than a year ago, and have tweaked it since. It *should*
be able to work in both Python2 and Python3.  It uses a GUI to select
different images, which is probably why I hadn't committed it until now,
since most of the code in my various git repositories are for command
line use.
Ignore built-in NA values

Mainly, this fucks up the nan gene.
Merge branch 'LowVolume'

Conflicts:
	AnalyzeFoldChanges.py
	MakeSummaryTable.py
	Makefile
	configure
Include FilterOrthologs from LowVolume branch
Merge branch 'master' of github.com:petercombs/EisenLab-Code

Conflicts:
	MakeSummaryTable.py