#####define segments, overlap, filename #######
shiftSize <- 5000
segmentSize <- 10000
fileName="ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes" # without type

#####compute how many segments we have#######
ina <- as.numeric(readLines(paste(fileName,"_mat.txt",sep=""),n=2))
snps <- ina[2]
over <- segmentSize%/%shiftSize
N1 <- snps%/%shiftSize
endRunA <- (N1-over+2)

startRun=1
endRun=640
prefixPath=""
sparseMatrixPostfix="_mat"
annotPostfix="_annot.txt"
samplesPostfix="_samples.txt"
samples=0

#snps and samplesN
load(file=paste(fileName,"_All",".Rda",sep=""))

#indi
load(file="individuals.Rda")



for (posAll in startRun:endRun)  {

start <- (posAll-1)*shiftSize
end <- start + segmentSize

if (end > snps)  {

  end <- snps
}


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)  {

noSample <- mergedIBD[[ibdC]]$noSamples



labelsEUA <- indi[noSample,2]
labelsNAA <- indi[noSample,1]
labelsTechA <- indi[noSample,4]
labels_ALLA <- paste(labelsNAA,labelsEUA,sep="_")

mergedIBD[[ibdC]]$countrySamples <- labelsEUA
mergedIBD[[ibdC]]$idSamples <- labelsNAA
mergedIBD[[ibdC]]$labelSamples <- labels_ALLA
mergedIBD[[ibdC]]$techSamples <- labelsTechA


} 
}
  
resHapFabia$mergedIBD <- mergedIBD
 
ibd2excel(resHapFabia$mergedIBD,paste(fileName,pRange,".csv",sep=""))

save(resHapFabia,annot,file=paste(fileName,pRange,"_resAnno",".Rda",sep=""))







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


noIBD <- length(mergedIBD)


if (noIBD>0)  {

for (ibdC in 1:noIBD)  {

noSample <- mergedIBD[[ibdC]]$noSamples



labelsEUA <- indi[noSample,2]
labelsNAA <- indi[noSample,1]
labelsTechA <- indi[noSample,4]
labels_ALLA <- paste(labelsNAA,labelsEUA,sep="_")

mergedIBD[[ibdC]]$countrySamples <- labelsEUA
mergedIBD[[ibdC]]$idSamples <- labelsNAA
mergedIBD[[ibdC]]$labelSamples <- labels_ALLA
mergedIBD[[ibdC]]$techSamples <- labelsTechA

}
  
}
  

save(mergedIBD,res,sPF,annot,resIBD1,resIBD2,mergedIBD1,mergedIBD2,file=paste(fileName,pRange,"_resIBD.Rda",sep=""))



}