First attempt at getting subset reads rolled in

Configure: Now generates a separate variable for the subset FPKMs to
generate

SubSample: Puts the subsetted reads into a subdirectory, rather than a
sibling directory. MakeSummaryTable now has the --in-subdirectory option
so that will work

Makefile: Various functions to subset the reads, sort them, run
cufflinks, and make the summary table.
Makefile tweak for subset FPKM calculations

Why does this work with all but not subset? My guess is something to do
with the prerequisites, but I'm not really sure.
AnalyzeFoldChange exposes more intermediate values
Differences for figure making

setcolor allows a black background and white foreground

AnalyzeFoldChanges now uses that, and also sets up an output directory
based on the name of the input file.

plotSMARTs uses the intermediate data from AFCs, and plots various
manual comparisons.
Parallelize SubSample
SubSample use Heap Push/Pop instead of Replace

It doesn't seem to be the major issue, but pushppop should be more
correct, due to the fact that it keeps overlaps.
Fixed a bug with no index, return values

If the bam file is not indexed, it won't be able to count the reads
properly, so it just goes through all of them once.  However, seek()ing
back to the beginning didn't work, so I'm now just re-opening the Bam
file.

I've also included return values from the sub-functions, so that I can
more closely scrutinize the results.
Switch to tophat for mapping

Perhaps this is the problem.  Many of these changes were imported, by
hand, poorly, from the current (as of 5/9/2014) branch of Fall2012. It
just doesn't look like it, 'cause I copy/pasted from a different folder,
rather than directly doing a merge.
Add in REFDIR variable everywhere in Makefile
Compute output directory relative to input file
Subset-dependent changes

Makefile was depending on things to exist that didn't always, and so was
getting messed up, requiring a two-step call to make.

Also gives SubSample the option to look in a specific directory (allows
Makefile to use different $ANALYSIS_DIR
Better expunge 'analysis' from magic strings