str1 <- scan(file = "out.txt", what = "character", sep = "", skip = 4, nlines = 1)
substr(str1, 1,1)
substr(str1, 10,10)

str2 <- scan(file = "out.txt", what = "character", sep = "", skip = 7, nlines = 1)
stA <- strsplit(str2, ",")
k <- as.numeric(stA[[1]][3])+1


snvN1 <- scan(file = "struc.txt", what = "character", sep = " ", skip = 0, nlines = 1)
l1 <- length(snvN1)-1
snvN1<-snvN1[-(l1+1)]


pos1 <- scan(file = "struc.txt", what = "numeric", sep = " ", skip = 1, nlines = 1)
pos1<-pos1[-(l1+1)]

pos1 <- as.numeric(pos1)

refT <- vector("character",l1)
for (i in 1:l1) {
  if (i==1) {
    pos1[1] <- k
  } else {
    t <- pos1[i]+k
    pos1[i] <- t
    refT[i] <- substr(str1, t,t)
  }
}


dataG <- read.table(file="struc.txt", header = FALSE, colClasses = "character",sep = " ",skip = 2)
 
dataG <- dataG[,c(-1,-2)]
dataG <- dataG[,-(l1+1)]


ref <- vector("character",l1)
alt <- vector("character",l1)
hap <- matrix("integer",nrow=10000,ncol=l1)
a3 <- vector("integer",l1)

for (i in 1:l1) {

  a1 <- dataG[,i]
  a2 <- table(a1)
  
  if (length(a2)==1) {
    ref[i] <- names(a2)
    alt[i] <- names(a2)
    hap[,i] <- as.vector(rep(0,10000))
  } else {
    na <- names(a2)

    a3 <- as.vector(rep(0,10000))

    if (a2[1]>a2[2]) {
      a3[which(a1==na[2])] <- 1
      ref[i] <- na[1]
      alt[i] <- na[2]
    } else {
      a3[which(a1==na[1])] <- 1
      ref[i] <- na[2]
      alt[i] <- na[1]
      
    }
    hap[,i] <- a3
  
  }

}

hap <- matrix(as.numeric(hap),nrow=10000,ncol=l1)


# alleleI = hap
# alleleN = dataG

save(dataG,alt,ref,pos1,hap,file="res1.Rda")