Have an SVG heatmap file
Changes brought in from Spring2013

This *should* make it so that the master branch is fairly generalizable
for new sequencing projects. Ha. Ha. I'll believe it when I see it.
Allow option to filter out low-read counts

Samples with low reads (less than, say, 500k) will be a lot noisier and
are known to have lower correlation with other samples. This allows an
option to MakeSummaryTable that does not combine them into the final
table, though they are still computed using tophat, and nothing is
renumbered.
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
Merge branch 'master' into Spring2013

Conflicts:
	MakeSummaryTable.py
	Makefile
	PlotUtils.py
	analyze.make
	configure
Strip out samples with fewer than 100k reads