#create x randomized hash index for simulations

#create hash table for simulation
sampleSize <- 22899009; #as.numeric(pain2[1,4]);
for(i in 1:8) {
  hashMatrix1 <- matrix(NA, nrow=sampleSize, ncol=25);
  for(j in 1:25){
    cat('.')
    hashMatrix1[,j]<-sample(1:sampleSize);
  }
  write.table(hashMatrix1, paste('/media/sdb/illumina/gr.study/coord/pain2/hashInd_pain2',i,'.txt',sep=''), sep='\t', row.names=F, col.names=F);
  hashMatrix1<-NULL;  
  cat(i,"\n")
}



#lane repeats
#counts
#SNL 1:
   #ALL: 29732811
   #L1:   6991922
   #L3:   8169514
   #L6:   7566501
   #L8:   7004874
#CNT 1:
  #ALL: 22889564
  #L2:   7744611
  #L4:   7695516
  #L7:   7458882
#SNL 2: 
  #ALL: 31470808 
  #L1:   7238113
  #L3:   8313014
  #L6:   8277140
  #L8:   7642541
#CNT 2:
  #ALL: 24584778
  #L2:   8113974
  #L4:   8248849
  #L7:   8221955
#create file with random permutated indexes
UMR<-c(29732811,6991922,8169514,7566501,7004874,
       22889564,7744611,7695516,7458882,
       31470808,7238113,8313014,8277140,7642541,
       24584778,8113974,8248849,8221955
)
fileName<-c("pain1_lane_ALL.hash.txt","pain1_lane1.hash.txt","pain1_lane3.hash.txt","pain1_lane6.hash.txt","pain1_lane8.hash.txt",
            "pain2_lane_ALL.hash.txt","pain2_lane2.hash.txt","pain2_lane4.hash.txt","pain2_lane7.hash.txt",
            "pain3_lane_ALL.hash.txt","pain3_lane1.hash.txt","pain3_lane3.hash.txt","pain3_lane6.hash.txt","pain3_lane8.hash.txt",
            "pain4_lane_ALL.hash.txt","pain4_lane2.hash.txt","pain4_lane4.hash.txt","pain4_lane7.hash.txt"
);


for(i in 1:length(UMR)) {
  sampleSize<-UMR[i];
  hashMatrix1 <- c(1:sampleSize);
  hashMatrix1 <-sample(1:sampleSize);
  write.table(hashMatrix1, paste('/media/sdb/illumina/gr.study/coord/hash/',fileName[i],sep=''), sep='\t', row.names=F, col.names=F);
  hashMatrix1<-NULL;  
  cat(i,"\n")
}