Add Beacon's AlleleCount

This is a piece of code that I wrote some time ago while I was working on the AMPLab beacon. It generates text files with frequencies of the alleles observed in an ADAM converted vcf file.
Instead of having the filter, make chooseAllele return an option, and change the map into a flatMap.

Also, by convention we use camel case without underscores, so reduced_Variants should just be reducedVariants.