RescueAmbiguous now works on any species

Thanks to Steven Kuntz!
Merge in changes from ZeldaAnalysis

Changes in various files:
* CountAllReads:
   - Allow command line options for alternate directory
* PlotUtils:
   - svg_heatmap takes an "index" option for relabelling the rows (I
     think)
   - fixed an alignment bug
* configure:
   - Redo the handling of yeast files to deal with merged slices
   - Specify an optional RunConfig file
Grab more files from ZeldaAnalysis
Also get PeakFinder
Add a pandas option to PointCloudReader

Like with numpy, this will gracefully fall back if pandas is not available.  If
it is, it will return a Panel with the same axes, but fortunately the genes can
be labelled.
Add a pandas option to PointCloudReader

Like with numpy, this will gracefully fall back if pandas is not available.  If
it is, it will return a Panel with the same axes, but fortunately the genes can
be labelled.
Fix time bug in PointCloudReader

Although each time point was internally consistent, they were being given in
the wrong order in the final output array.  Stupid me for not sorting the set!
Merge branch 'master' of github.com:petercombs/EisenLab-Code

Conflicts:
	PointClouds.py
Add in a get_neighbors function to PointCloudReader

Turns out that the file kept a list of the neighbors of each cell, and I just
didn't know about it.  It's actually pretty easy to get that list out.

Also rejigger the numbering in pandas Panels so that it agrees with the id's for each cell.
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.
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