startRun <- 0
endRun <- 639

#startRun <- 0
#endRun <- 639


load(file="/seppdata/sepp/linkage/release/annotation/individuals.Rda")

lengthAll <- 3201157
shift <- 5000
intervallAll <- 10000
over <- intervallAll%/%shift

N1 <- lengthAll%/%shift
endRunAll <- (N1-over+1) # 639

source("/seppdata/sepp/linkage/release/scripts/funct.R")

allCount <- 0
allCount1 <- 0

for (posAll in (startRun+1):(endRun+1))  {

start <- (posAll-1)*shift
end <- start + intervallAll

if (end > lengthAll)  {

  end <- lengthAll
}

rm(mergedIBD)
rm(resIBD1)
rm(resIBD2)
rm(mergedIBD1)
rm(mergedIBD2)

  
pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="")

load(file=paste("resIBD_chr1",pRange,".Rda",sep=""))


noIBD <- length(mergedIBD)


if (noIBD > 0) {
  


for (ibdC in 1:noIBD)  {

allCount <- allCount + 1

snpPositions <- mergedIBD[[ibdC]][[15]]
numberSnps <-  mergedIBD[[ibdC]][[7]]
length <- snpPositions[numberSnps] - snpPositions[1]
mergedIBD[[ibdC]][[5]] <- length


cat(allCount," out of 222246\r")

}
}

noIBD <- length(mergedIBD1)


if (noIBD > 0) {
  


for (ibdC in 1:noIBD)  {


snpPositions <- mergedIBD1[[ibdC]][[15]]
numberSnps <-  mergedIBD1[[ibdC]][[7]]
length <- snpPositions[numberSnps] - snpPositions[1]
mergedIBD1[[ibdC]][[5]] <- length



}
}

noIBD <- length(mergedIBD2)


if (noIBD > 0) {
  


for (ibdC in 1:noIBD)  {


mergedIBD2[[ibdC]][[5]] <- length
snpPositions <- mergedIBD2[[ibdC]][[15]]
numberSnps <-  mergedIBD2[[ibdC]][[7]]
length <- snpPositions[numberSnps] - snpPositions[1]
mergedIBD2[[ibdC]][[5]] <- length


}
}

save(mergedIBD,resIBD1,resIBD2,mergedIBD1,mergedIBD2,file=paste("resIBD_chr1",pRange,".Rda",sep=""))

ibd2excel(mergedIBD,paste("ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,".csv",sep=""))


load(file=paste("resIBD_chr1",pRange,"annot.Rda",sep=""))


noIBD <- length(IBDannot)


if (noIBD > 0) {
  


for (ibdC in 1:noIBD)  {


snpPositions <-IBDannot[[ibdC]][[15]]
numberSnps <-  IBDannot[[ibdC]][[7]]
length <- snpPositions[numberSnps] - snpPositions[1]
IBDannot[[ibdC]][[5]] <- length



}
}

save(IBDannot,file=paste("resIBD_chr1",pRange,"annot.Rda",sep=""))

ibd2excel(IBDannot,paste("ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_annot.csv",sep=""))


}