Added GATK 3.2
A version of the 3D7 reference that has the same order as the aligned PacBio file.  The apicoplast contig has purposely been modified to be shorter than it appears in the PlasmoDB 9.0 reference.  We can get away with this because we will not be doing any analyses involving the apicoplast.
Added INDIANA jar
Control script
Ignore the cache/ directory
Show every 5000-th base in the coverage-on-ideogram plot.