Convert a genind object to a genambig object from polsay

gen2polysat.R

gen2polysat <- function(gen, newploidy = gen@ploidy){
  if (!require(polysat)){
    stop("User needs polysat installed")
  }
  gen   <- recode_polyploids(gen, newploidy)
  gendf <- genind2df(gen, sep = "/", usepop = FALSE)
  gendf <- lapply(gendf, strsplit, "/")
  gendf <- lapply(gendf, lapply, as.numeric)
  ambig <- new("genambig", samples = indNames(gen), loci = locNames(gen))
  for (i in names(gendf)){
    res <- lapply(gendf[[i]], function(x) ifelse(is.na(x), Missing(ambig), x))
    Genotypes(ambig, loci = i) <- res
  }
  return(ambig)
}