Bumps used bwa up to .7.something
Increases threading/cores for HaplotypeCaller
Changes to new hard coded fast scratch dir

bwa_mem wrapper makes a per job temp dir as well

I should change this to an option of some sort
Adds a genome version to haplo qsub task

Right now then this means you can do 25 human chr or the mouse chr
number that I can't remember right now

Bumps version number
Makes dbsnp optional
Adds -t/--tmp option for :tmp_dir_base to name tmp

No more hard coded crap. We can now by run or sample or big group name a
local, a remote or what ever we want (/dev/null is pretty fast tmp)