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 branch 'master' into ZeldaAnalysis

configure: Kept the ZeldaAnalysis branch, this has all the tweaks I made
to make combining adjacent slices work well

MakeSummaryTable: Mainly kept the master, since this has the new code
for doing read-abundance filtering

Makefile: Mainly the master, but kept changes specific to ZeldaAnalysis
branch

PlotUtils: Combined the options that I had added in both cases.

Conflicts:
	MakeSummaryTable.py
	Makefile
	PlotUtils.py
	configure