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# fastacc: Fast Allele in Common Count
#
# Computes the number of common alleles between a target and a database
#
fastacc <- function(target, database)
{
#
# Check arguments:
#
if(!is.raw(target)) stop("raw vector expected for target")
noc <- length(target)
if(noc < 1) stop("empty target")
if(!is.raw(database)) stop("raw vector expected for database")
if(length(database) %% noc != 0) stop("database length must be a multiple of target length")
#
# n is the total number of entries in DB
#
n <- length(database)/noc
n <- as.integer(n)
#
# Pre-compute the table giving the number of bits per octet
#
bits_in_char <- sapply(as.raw(0:255), function(x) sum(as.integer(rawToBits(x))))
bits_in_char <- as.integer(bits_in_char) # just to make sure
res <- .Call("fastacc", bits_in_char, target, database, noc, n, PACKAGE = "seqinr")
return(res)
}
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