b) Several improvements to BeagleOutputToVCFWalker:
1. If a Hapmap input track is provided (e.g. -B comp,VCF,file), Hapmap sites will be annotated with Hapmap Allele count and allele frequency (key ACH, AFH).
2. If probability of correct genotype is lower than ncthr (optional argument provided by user, default = 0.0), walker will keep original calls instead of using Beagle calls.
3. Instead of annotating just whether Beagle had modified a site, annotate instead HOW MANY genotypes in a site were actually changed by Beagle.
All three improvements are mostly for debugging and analysis only.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3769 348d0f76-0448-11de-a6fe-93d51630548a
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