startRun <- 0
endRun <- 639
lengthAll <- 3201157
shift <- 5000
intervallAll <- 10000
runIndex=""
all=222246

load(file=paste("resDups.Rda",sep=""))
load(file="../individuals.Rda")




over <- intervallAll%/%shift

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

allCount <- 0
allCount1 <- 0

HapPos <- c()
HapLength <- c()


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

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

if (end > lengthAll)  {

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


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

noIBD <- length(IBDannot)

if (noIBD>0)  {

for (ibdC in 1:noIBD)  {

allCount <- allCount + 1

if (!dups[allCount]) {

allCount1 <- allCount1 + 1

ibdPos <-  IBDannot[[ibdC]][[4]]
HapPos <- c(HapPos,ibdPos)

ibdLength <- IBDannot[[ibdC]][[5]] 
HapLength <- c(HapLength,ibdLength)

}

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

}

}


}


write.table(HapPos,file=paste("HapPos",runIndex,".txt",sep=""))
write.table(HapLength,file=paste("HapLength",runIndex,".txt",sep=""))
            
save(HapPos,HapLength,file=paste("HapPos",runIndex,".Rda",sep=""))