library(GenomicRanges)

###################################################

for (noIm in 1:noImplanted) {
  if (noIm==1) {
    implRange <- GRanges(seqnames="chr", ranges=IRanges(start=intervalImp[[noIm]][,1], end=intervalImp[[noIm]][,2]))
    implSamp1 <- implG[[noIm]]
  } else {
    implRange <- c(implRange,GRanges(seqnames="chr", ranges=IRanges(start=intervalImp[[noIm]][,1], end=intervalImp[[noIm]][,2])))
    implSamp1 <- c(implSamp1,implG[[noIm]])
  }
}

implSamp <- unique(implSamp1)


###################################################

allSamp <- c()
allSnps <- c()
rrS <- c(0)

foundAll <- matrix(0,samplesN,snps)


if (nrow(resGermline)>0) {
  samp1V <- as.vector(unlist(resGermline[1]))
  samp2V <- as.vector(unlist(resGermline[3]))
  beginV <- as.vector(unlist(resGermline[8]))
  endV <- as.vector(unlist(resGermline[9]))
  beginV[which(beginV==0)] <- 1

lengthIBDV <- pos[endV] - pos[beginV]

w1 <- which(lengthIBDV>shunkFact*ShunkLength)
w2 <- which(lengthIBDV<1.2*1000*lengthI)

w3 <- intersect(w1,w2)

samp1V <- samp1V[w3] 
samp2V <- samp2V[w3]
beginV <- beginV[w3]
endV <- endV[w3]

allSamp <- union(samp1V,samp2V)


gr <- GRanges(seqnames="chr", ranges=IRanges(start=beginV, end=endV))

gr1 <- reduce(gr)
theSnps <- rep(0,snps)

sG <- start(gr1)
eG <- end(gr1)

for (i in 1:length(sG)) {
range <- sG[i]:eG[i]
theSnps[range] <- 1 
}
  
allSnps <- which(theSnps>0)

Rsum <- function(i) {
sel <- which(samp1V == i | samp2V == i)
sum(width(reduce(gr[sel])))
}


rrS <- sapply(1:samplesN,Rsum)


R1 <- which(gr %in% implRange)

R21 <- which(samp1V %in% implSamp)
R22 <- which(samp2V %in% implSamp)

R2 <- union(R21,R22)

RA <- intersect(R1,R2)

samp1V <- samp1V[RA] 
samp2V <- samp2V[RA]
beginV <- beginV[RA]
endV <- endV[RA]


  
gr2 <- gr[RA]

  
Psum <- function(i) {
sel1 <- which(implSamp1== i)
if (length(sel1)>0) {
sel <- which(samp1V == i | samp2V == i)
grn <- intersect(gr2[sel],implRange[sel1])
sum(width(reduce(grn)))
} else {
  0
}
}

rrP <- sapply(1:samplesN,Psum)



}
  
detected <- sum(rrS)

all <- samplesN*snps
Pos <- sum(implantT)
  
trueP <- sum(rrP)