if(is.null(names(phasefiles))) names(phasefiles) <- 1:length(phasefiles)

for(chr in names(phasefiles)){

print(phasefiles[chr])

phase <- readLines(phasefiles[chr])

nind <- as.integer(phase[2])

nsites <- as.integer(phase[3])

pos <- unlist(strsplit(phase[4], split = " "))

i <- match("P", pos)

if(is.na(i))

pos <- as.integer(pos)

else

pos <- as.integer(pos[-1])

mat <- phase[6:length(phase)]

gt <- as.integer(unlist(strsplit(mat[1], split="")))

stopifnot(length(pos)== nsites)

stopifnot(length(pos)==length(gt))

bim <- make_bim( n = nsites )

bim$chr <- chr

bim$pos <- pos

bim$id <- paste0(chr, "_", pos)

fam <- make_fam( n = nind )

G <- sapply(1:length(mat), function(i){

gt <- as.integer(unlist(strsplit(mat[i], split="")))

})

G <- G[, seq(1, ncol(G), 2)] + G[, seq(2, ncol(G), 2)]

fileplink <- paste0(output, ".", chr)

o <- write_plink(fileplink, G, bim, fam, verbose = FALSE)

}