Add very basic review dialog for VCF. IDE is importing gatk classes, so it doesn't compile in ant just yet
Add GenotypeType combo box. Have Genotype.getType return a GenotypeType, getTypeString returns a string
Make VariantMenu a bit more user-friendly in its handling of VariantReviewDialog.

 Only provides the option is SHOW_VARIANT_REVIEW=true in system property (or preferences). DB spec can be specified with system property as well.

 Add "getPersistent" methods, which look for preferences in both pref file and system properties. Saves system property to preferences if found. Intended usecase is features only usable by certain groups but not intended for all of IGV.
Include na12878kb.jar (and update vcf.jar, StingUtils.jar) so we can run VariantReviewDialog without linking to gsa-unstable

na12878kb.jar was built on this developers machine, from gsa-unstable bbff7a4292bd04578fc05467ce0017ce17cbaf3c.
See IGV repo, commit 31cc4b09abfd6a79e70e8132c4bc0113ba496389 for details on vcf.jar and StingUtils.jar.
Have VariantReview work on site, rather than sample. Check for preferential sample and use that data, if multiple samples found (and none preferential) with contradictory data, set things to unknown
Update na12878kb.jar so it uses production db
set reviewed = true for genotype written to db
Merge branch 'master' into MongoGSA

Conflicts:
	src/org/broad/igv/sam/AlignmentTrack.java
Disable "Submit Review" when clicking on sample name
Some refactoring to put most things having to do with variant reviewing in VariantTrack
Add NA12878KBReview implements FeatureSource. In theory should be able to query db when called correctly, provided we find a way to create a GenomeLocParser
Update na12878kb.jar, sam to version 1.81, include picard
Finish NA12878KBReviewSource, add unit test. Created test adding and getting variant reviews. Test has no facility for starting/stopping mongodb, so we just use assumptions to avoid superfluous failures
Have variant renderer more properly detect genotype not found for sample, and log it
Add auto-loading of variant review track when vcf loaded which contains appropriate sample name.
Change how VariantTrack review is loaded

Now we flip a boolean switch so we only load one of these tracks. Also put it above the loaded vcf file
Merge branch 'master' into MongoGSA

Conflicts:
	src/org/broad/igv/sam/AlignmentTrack.java
Move VariantReviewDialog and associated classes to own package. Want to use it as an example for creating/demonstrating plugin architecture
Merge branch 'master' into MongoGSA
Refactor how we load VariantContext reviews, to better separate it from main IGV. Add an additional API hook for adding a track.
Need to add hook for adding to context menu, and then we should be good