#' @keywords internal
exclude.vloop.sites <- function(S, site_list) {
if (class(S) != "swarmtools")
stop("ERROR: Unexpected status for arguments to exclude.vloop.sites()")
# HXB2 sites for hypervariable loop regions; see Hraber et al. JVI 2014
vloop.sites <- c(132:152, 185:190, 396:410, 460:465)
S <- set.excluded.sites(S,
unique(c(S$refseq_lut$aln[which(S$refseq_lut$l %in% vloop.sites |
S$refseq_lut$r %in% vloop.sites )]),
S$excluded_sites))
return ( S )
}
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