random.msat <- function(N, a, f, map, freq) {
delta.dist <- diff(map$distance)
# treat properly the change of chromosome
I <- cumsum(rle(map$chr)$length)
I <- I[-length(I)]
delta.dist[I+1] <- -1
a <- rep_len(a, N)
f <- rep_len(f, N)
S <- Y <- NULL
for(i in seq_len(N)) {
s <- .Call('_Fantasio_simu0', PACKAGE = "Fantasio", delta.dist, a[i], f[i])
S <- cbind(S, s)
Y <- cbind(Y, .Call('_Fantasio_simu_geno', PACKAGE = "Fantasio", s, freq))
}
list(S = S,
X = new("msat.matrix", ncol = nrow(map), nrow = N, ped = data.frame(fam = seq_len(N), id = 1, father = 0, mother = 0, sex = 1, pheno = 2),
msat = Y, map = map, freq = freq))
}
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