Work on adding bwa mem
Adding Picard/GATK comp. option
Making Bwa type a option in DNABPVC and ...

... making sure that the Haloplex pipeline remains stable with bwa aln.
Argument not input for string
Updating bwa versions a samtools

Making use of multi-thread capabilites of samtools and bwa.
Update bwa and samtools...

... fixing corresponding tests.
Tuning intermediate files in bpvc.
Merged files can optinally be removed.
8G per thread (not 8G*nbrOfThreads)
Make sure that aligments are not intermediate...

... if we are running only the raw aligments.
Lowering samtools sort from 8G to 7G per thread
Trying to slove bwa mem memory usage issue.
Trying to get a whole node
Renaming GATKOptions to GATKConfig for concistency
Updating to scala 2.10 to follow Queue
General refactoring and cleaning up...

... in particular VariantCalling options have gotten it's own case class for encapsulating the options. Hopefully this will make it easier to set reasonable defaults in the future.
Setup script goes for gatk main repo and uses mvn
Maven instead of Ant in readme
Work on bringing in the Haplotype caller
Removing unsed method from SetupXMLReaderAPI