Estimate Std Dev in BayesMatch
In CalculateAbundances, do a No-bcd run

Due to multiple testing, and especially due to the fact that it goes up
by the square of the number of things we're testing, including the bcd
samples in one round really kills our ability to detect.

Furthermore, it looks like we're not going to look at the bicoid data in
the paper.
IPython Notebook to make figure 2 of the paper

This is the heatmap sorted by center-of-mass
For Figure1, do analyses based on no bicoid

This involves using differently named files, so minor changes there.
Also cosmetic changes to the figures, especially better usage of the
BDGP annotations.
Cosmetic changes to output from BayesMatch
Add VLines to figure 1

These are to indicate approximate slice boundaries.
Exclude genes with low expression from figure 1
Clear output in RunBayesMatch
Manually remove some images at wrong stage
More Exploration
Ignore more non-code files
Remove old, unused code

It should still be in the commits, but I don't know how half this stuff
works anymore, and would probably end up rewriting it anyways.
Clean up MapReads
Switch MapReads to STAR
Run off the actual data, not the test set
the correct STAR parameters to use
Don't create an assigned.bam, in addition to the assigned_species.bam files
Remove non-core slice-seq files

Lots of these either no longer serve a purpose, or are for specific
iterations of the analysis which the general code is no longer serving.
Rework CheckCoverage

Now goes solely based on exons, which, among other things, means it
*should* now work from the GFF file as well (although the smaller GTF
file is always nice)

Also adds a progress bar.  Because I'm impatient.
Minor tweaks to heatmap plotting