Nothing
prepareForHDF5 <- function( counts, reference ){
stopifnot(class(reference) == "DNAString")
ret <- list()
ret$Counts <- counts[-c(grep("[-+]", dimnames(counts)[[1]])),,,,drop=FALSE]
ret$Coverages <- apply( ret$Counts, c(2,3,4), sum)
ret$Deletions <- apply( counts[c("-.front","-.mid","-.back"),,,,drop=FALSE], c(2,3,4), sum )
ret$Insertions <- apply( counts[c("+.front","+.mid","+.back"),,,,drop=FALSE], c(2,3,4), sum )
ref <- encodeDNAString( reference ) + 1
for( base in 1:4){
idxs = which( ref == base )
for( strand in 1:2){
ret$Counts[base,, strand,idxs] <- 0
ret$Counts[base + 4,, strand,idxs] <- 0
ret$Counts[base + 8,, strand,idxs] <- 0
}
}
ret$Reference <- ref - 1 #the tally file encodes the reference as A=0,C=1,G=2,T=3
return(ret)
}
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