load("dups.Rda")
load("analyzeResult.Rda")
load(file="/seppdata/sepp/linkage/kpgp/denisovaHg19KPGPChr1.Rda")
library(hapFabia)
library(fabia)
#source("prepareAncientGenome.R")
#source("plotAncientGenomes.R")

shiftSize <- 5000
segmentSize <- 10000
fileName="KPGP1000_chr1" # without type


startRun <- 1
endRun <- 633

runIndex=""


lengthAll <- 3167651
shift <- 5000
intervallAll <- 10000
over <- intervallAll%/%shift

N1 <- lengthAll%/%shift
endRunAll <- (N1-over+2) # 639


res <- c()

allCount <- 0
allCount1 <- 0

for (posAll in startRun:endRun)  {

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(fileName,pRange,"_resAnno",".Rda",sep=""))
mergedIBD <- resHapFabia$mergedIBD 


noIBD <- length(mergedIBD)


if (noIBD > 0) {
  


for (ibdC in 1:noIBD)  {

allCount <- allCount + 1

if (!dups[allCount]) {


l1 <-mergedIBD[[ibdC]][[15]] 

res <- union(res,l1)

} 

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

}
}


}


print(length(res))

save(res,file=paste("haplotypeSNVs",runIndex,".Rda",sep=""))