Nothing
score = function(prof1, prof2, bWildCard = FALSE, bRareAllele = FALSE, nRareCode = 99) {
## assumes that profiles have id as the first entry and then 2*n alleles
nLoci = (length(prof1) - 1)/2
i1 = which(!(nRareCode %in% prof1[(2 * (1:nLoci)):(2 * (1:nLoci) + 1)]) && (prof1[2 * (1:nLoci)] >
prof1[2 * (1:nLoci) + 1]))
if (any(i1)) {
tmp = prof1[2 * i1]
prof1[2 * i1] = prof1[2 * i1 + 1]
prof1[2 * i1 + 1] = tmp
}
i2 = which(!(nRareCode %in% prof2[(2 * (1:nLoci)):(2 * (1:nLoci) + 1)]) && (prof2[2 * (1:nLoci)] >
prof2[2 * (1:nLoci) + 1]))
if (any(i2)) {
tmp = prof2[2 * i2]
prof2[2 * i2] = prof2[2 * i2 + 1]
prof2[2 * i2 + 1] = tmp
}
# mikl scores = .Call('score_cpp')
scores = score_rcpp(prof1 = as.integer(prof1[-1] * 10), prof2 = as.integer(prof2[-1] * 10),
numLoci = nLoci, useWildCard = bWildCard, useRareAllele = bRareAllele)
g1 = paste(prof1[2 * (1:nLoci)], prof1[2 * (1:nLoci) + 1], sep = "/")
g2 = paste(prof2[2 * (1:nLoci)], prof2[2 * (1:nLoci) + 1], sep = "/")
g1 = gsub(as.character(nRareCode), "R", g1)
g2 = gsub(as.character(nRareCode), "R", g2)
return(data.frame(g1 = g1, g2 = g2, score = scores))
}
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