Move printing out of function for MP

I think it wasn't printing the output because of the different threads.
Moving the print statements to the single-threaded part of the code
seems to have worked.
Configure now tries multiple glob patterns for reads

In theory, I could have a list of them to try.  In practice, I probably
won't.
Tweaks to analyze dependencies
Don't use the subsetted reads in Analyze*

It doesn't seem to make a huge difference, and I haven't (yet) automated
the sub-setting.
Tweaks to AnalyzeFoldChanges for interactive exploration

Basically, I also want to save out the slopes, to see how those
correlate.  I'm also ignore the subsetting for the moment, since it
doesn't seem to have a huge effect anyways.
Start looking at cutoff FPKM values