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
More work on HaplotypeCaller wf
Making variant caller to use an option...

... with the Haplotype caller as the default.
Fixed pattern matchin problem for vc option
Adding recalibration for HC wf
Fixed typo in comment
Lower maximum ram limit for MarkDuplicates.
Maximum bam compression level...

... in dedup.
VariantCat demands vcf format.
Maximum compression ratio in bams from GATK-tools
Updating BP VQSR to fit HC WF
Updating VQSR for indels according to BP
Updating to 2.8 GATK bundle
Fewer tranches in VQSR