R/compare_check.R

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

#' Compare top and bottom sequneces and report errors.
#'
#' @param top top sequence
#' @param bottom sequence
#' @export
compare_check <- function(top, bot) {
  ret <- list(
    skip = NA,
    stut = NA,
    error = NA,
    error_sum = 0
  )

  topMT <- sq_match(top, "T")
  botMT <- sq_match(bot, "T")
  topMA <- sq_match(top, "A")
  botMA <- sq_match(bot, "A")
  topMC <- sq_match(top, "C")
  botMC <- sq_match(bot, "C")
  topMG <- sq_match(top, "G")
  botMG <- sq_match(bot, "G")
  topMT <- sq_match(top, "T")
  botMT <- sq_match(bot, "T")

  ret$skip <-
    topMA & botMA |
      topMG & botMG |
      topMA & botMG |
      topMG & botMA |
      topMA & botMC |
      topMC & botMA

  ret$stut <- topMT & botMT

  ret$error <- ret$skip | ret$stut
  ret$error_sum <- sum(ret$error)
  return(ret)
}