Nothing
"mismatches"<-function(X.list, G, mm.tol=999){
noff<-length(X.list$X)
ndam<-c(unlist(lapply(X.list$X,function(x){length(x$dam.id)})))
nsire<-c(unlist(lapply(X.list$X,function(x){length(x$sire.id)})))
if(is.genotype(G[[1]])){
offid<-as.numeric(names(X.list$X))-1
damid<-c(unlist(lapply(X.list$X,function(x){x$dam.id})))-1
sireid<-c(unlist(lapply(X.list$X,function(x){x$sire.id})))-1
nind<-length(G[[1]])
nloci<-length(G)
G<-GtoC(G)
mmD<-rep(0,sum(ndam))
mmS<-rep(0,sum(nsire))
output<-.C("mismatches",
as.integer(nind),
as.integer(noff),
as.integer(ndam),
as.integer(nsire),
as.integer(nloci),
as.integer(offid),
as.integer(damid),
as.integer(sireid),
as.integer(mmD),
as.integer(mmS),
as.integer(G))
sD<-1
for(i in 1:noff){
X.list$X[[i]]$mmD<-output[[9]][(sD-1)+1:(ndam[i])]
sD<-sD+ndam[i]
dremove<-X.list$X[[i]]$dam.id[which(X.list$X[[i]]$mmD>mm.tol)]
dremove<-which(X.list$X[[i]]$restdam.id%in%dremove==TRUE)
if(length(dremove)>0){
X.list$X[[i]]$restdam.id<-X.list$X[[i]]$restdam.id[-dremove]
}
}
sD<-1
for(i in 1:noff){
X.list$X[[i]]$mmS<-output[[10]][(sD-1)+1:(nsire[i])]
sD<-sD+nsire[i]
sremove<-X.list$X[[i]]$sire.id[which(X.list$X[[i]]$mmS>mm.tol)]
sremove<-which(X.list$X[[i]]$restsire.id%in%sremove==TRUE)
if(length(sremove)>0){
X.list$X[[i]]$restsire.id<-X.list$X[[i]]$restsire.id[-sremove]
}
}
}else{
for(i in 1:noff){
X.list$X[[i]]$mmD<-rep(0,ndam[i])
X.list$X[[i]]$mmS<-rep(0,nsire[i])
}
}
X.list
}
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