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
Merge branch 'Spring2013' of https://github.com/petercombs/EisenLab-Code into Spring2013
Track paired-end reads properly, and allow multiple sequence directories

At some point, I changed the search string for the first end, but not
the second, and that meant that I was only doing single-end mapping. As
part of this, I include a warning (technically, just a print
statement... maybe this should go to stderr) if it doesn't find the
second end as well. Also, I sort both ends, so there's less room for
error if things get globbed in different orders (this appeared to have
been a problem)

Also, since the first round of sequencing the data in this batch didn't
work, I have a sequence and a sequence2 directory. Adding a * in the
glob path after sequence now catches both.
Merge branch 'Spring2013' of github.com:petercombs/EisenLab-Code into Spring2013
Force creation of image directory if not already present
Update dynamic range to 10,000