startRun <- 0
endRun <- 639
runIndex=""

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

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



avibdLength <- list()
avibdPos <- list()
count <- 0

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)
count <- count + noIBD


if (noIBD>0)  {

avibdPos[[posAll]] <-  sapply(IBDannot,function(x) {x[[4]]}  , simplify=FALSE)

avibdLength[[posAll]] <-  sapply(IBDannot,function(x) {x[[5]]}  , simplify=FALSE)

}
}


ibdPos <- unlist(avibdPos)
ibdLength <- unlist(avibdLength)

ibdSim <- cbind(ibdPos,ibdLength)

dups <- duplicated(ibdSim)

un <- which(dups==FALSE)



length(ibdPos)
length(ibdLength)

length(un)
count

save(dups,un,file=paste("resDups",runIndex,".Rda",sep=""))