Strip out pooled species from makefile and configure
Fix references to MELFASTA2
Use shared memory for STAR
Update FlyBase reference to 6.01
Option for custom base name of SummaryTable
Merge branch 'master' into BcdRNAi

Conflicts:
	Makefile
Tweak readfile glob in configure

VCGSL keeps changing the exact format on me.  I got it really close this time, though!
Drop the 'all reads' from the configure script
Add option for a different bamfile for looking at minimum reads
Option for using 'default' as default colormap, instead of just None
Bring in JTreeView and DistroDiff from Zelda branch

Include changes to JTreeView to do the analyses I want, rather than the ones I've been doing.
Add Gene Map table to Makefile
Script to make a read summary table in LaTeX
Make an SVG file for every gene comparing the appropriate stages of WT and bcd-
Code to do simple {Bcd-,Zld-} vs WT comparisons
Automagically compute zld and bcd binding peaks
Recompute files better after version change
Update way to read out binding data
Calculate distances based on variable, rather than hard-coded cycle of interest
More changes to try to segment data into meaningful groups