hapmap2df <- function(x, gt.col = 2, first.col = 12, last.col = ncol(x)){
  ambi <- c("S","M","Y","R","K","W")
  names(ambi) <- c("A/T","C/G","A/C","G/T","A/G","C/T")
  genotypes <- levels(x[[gt.col]])
  major_alleles <- unlist(strsplit(genotypes, "/"))
  major_alleles <- major_alleles[1:(length(major_alleles)) %% 2 == 1]
  print(major_alleles)
  levels(x[[gt.col]]) <- major_alleles
  gtlevs <- unique(levels(x[[gt.col]]))
  print(gtlevs)
  x[c(gt.col, first.col:last.col)] <- lapply(x[c(gt.col, first.col:last.col)], as.character)
  x[first.col:last.col][apply(x[first.col:last.col], 2, `==`, x[[gt.col]])] <- 2
  x[first.col:last.col][apply(x[first.col:last.col], 2, `%in%`, gtlevs)] <- 0
  x[first.col:last.col][apply(x[first.col:last.col], 2, `%in%`, "N")] <- NA
  x[first.col:last.col][apply(x[first.col:last.col], 2, `%in%`, ambi)] <- 1
  out_matrix <- t(x[first.col:last.col])
  out_matrix <- apply(out_matrix, 2, as.numeric)
  colnames(out_matrix) <- x[[1]]
  rownames(out_matrix) <- names(x)[first.col:last.col]
  return(out_matrix)
}