1) Changed VCF/RodVCF to allow for inquiries to whether or not the site is novel; isNovel() looks at the ID field, and those members of the info field that indicate membership in dbsnp, hapmap2, or hapmap3; and if none can be found, returns true.
2) Changed VariantAnnotator to annotate hapmap2 and hapmap3, if you bind rods to it with those names. Works in the same way as DBSNP does -- if you give it a rod named "hapmap2" it'll annotate membership in it. -- Passes integration tests
3) Changed UnifiedGenotyper to do the same thing (since it uses Annotations as a subroutine) -- Passes integration tests
4) Changed MultiSampleConcordanceWalker to take a flag --ignoreKnownSites (or -novels) to examine concordance only on sites that are not marked as in dbSNP or in Hapmap in the variant VCF
5) Changed VCFConcordanceCalculator (the object MultiSampleConcordanceWalker runs on) to output Concordant_Het_Calls and Concordant_Hom_Calls separately, rather than combined as Concordant_Calls
6) AlleleBalanceHistogramWalker -- I don't know what i did to this thing. I've been jerry rigging System.outs to do stuff it was never really intended to do; so there's probably some dumb System.out.print("HI I AM AT LOCUS:"+loc) stuck somewhere. It compiles at any rate.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2724 348d0f76-0448-11de-a6fe-93d51630548a
8de6a8d246