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.
No, sorry, I mean adding a line (which will get printed out to the file) that prints something like
  chrom  position  refAllele  altAllele  allele1  allele2
(but with tabs instead of spaces) at the top of the file.