R/make_linker.R

In g-r-eg/fold2: Hairpin bisulphite sequence analyser.

#' Make a linker sequence from the batch sequence and barlength.
#'
#' @param batch batch sequence
#' @param barlen length of barcode sequence
#' @param side which side the hairpin is in relation to the main double stranded sequence
#' @return linker sequence
#' @export
make_linker <- function(batch, barlen, side = "right") {
  bar_empty <- rep("N", barlen)
  batch_conv <- batch
  batch_conv[batch_conv == "C"] <- "T"
  batch_revcompconv <- rev(sq_comp(batch))
  batch_revcompconv[batch_revcompconv == "C"] <- "T"
  if (side == "right") {
    return(c(batch_conv, bar_empty, batch_revcompconv))
  } else if (side == "left") {
    return(c(batch_revcompconv, bar_empty, batch_conv))
  }
}