res <- spfabia(paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),p=SS,alpha=0.03,cyc=50,spl=0,non_negative=1,write_file=0,norm=0,lap=100.0,samples=samples,iter=A,quant=0.01,lowerB=1.5,upperB=0.05*lii,eps=1e-5)


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



sPF <- samplesPerFeature(X=paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),samples=samples,lowerB=1.5,upperB=0.05*lii)

save(sPF,file=paste("sPF_15_005_chr1",pRange,".Rda",sep=""))


i <- 0
max_n <- ncol(res@L)
while ((i<max_n)&&(max(res@L[,i+1])>0.000001)) { i <- i +1 }

max_n <- i


off1 <- 0

resIBD1 <- getIBDs(res=res,sPF=sPF,annot=annot,chrom=1,labelsA=indiA,max_n=max_n,ps=ps,inteA=inteA,thresA=thresA,minSNPs=minSNPs,off=off1)


if ( length(resIBD1) > 1) {
  comp <- compareIBDres(resIBD1,simv="minD")

  mergedIBD1 <- mergeIBDres(resIBD1=resIBD1,resIBD2=NULL,comp=comp,cut=0.8) 
} else {
  
 mergedIBD1 <- resIBD1 
}




off2=inteA%/%2

resIBD2 <- getIBDs(res=res,sPF=sPF,annot=annot,chrom=1,labelsA=indiA,max_n=max_n,ps=ps,inteA=inteA,thresA=thresA,minSNPs=minSNPs,off=off2)


if ( length(resIBD2) > 1) {
  comp <- compareIBDres(resIBD2,simv="minD")

  mergedIBD2 <- mergeIBDres(resIBD1=resIBD2,resIBD2=NULL,comp=comp,cut=0.8) 
} else {
  mergedIBD2 <- resIBD2 
}

if ( length(mergedIBD1) > 0) {

  if ( length(mergedIBD2) > 0) {

    comp12 <- compareIBDres(mergedIBD1,mergedIBD2,simv="minD")

    mergedIBD <- mergeIBDres(resIBD1=mergedIBD1,resIBD2=mergedIBD2,comp=comp12,cut=0.8) 

} else {

mergedIBD <- mergedIBD1
}

} else {

  if ( length(mergedIBD2) > 0) {
    mergedIBD <- mergedIBD2
  } else {
    mergedIBD <- mergedIBD1
  }
  
  
}
  


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



#plotIBDs(IBD=mergedIBD,filename=paste("ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""))