R/fun_setting.R

In MANO-B/MicroSEC: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples

#' Mutated position search function.
#'
#' This function attempts to find the mutated bases in each read.
#'
#' @param pre The 5' side bases of the sequence for searching.
#' @param post The 3' side bases of the sequence for searching.
#' @param neighbor_seq Short reference sequence around the mutation.
#' @param neighbor_length The length from the mutation to the ends of the short
#'   reference sequence.
#' @param alt_length The length of altered bases.
#' @importFrom Biostrings substring

#' @return list(pre_search_length, post_search_length, peri_seq_1, peri_seq_2)
fun_setting <- function(pre, post, neighbor_seq, neighbor_length, alt_length) {
  peri_seq_1 <- substring(neighbor_seq,
                         neighbor_length + 1 - pre,
                         min(nchar(neighbor_seq),
                           neighbor_length + post + alt_length))
  peri_seq_2 <- substring(neighbor_seq,
                         neighbor_length + 1 - post,
                         min(nchar(neighbor_seq),
                           neighbor_length + pre + alt_length))
  return(list(pre, post, peri_seq_1, peri_seq_2))
}

# The following block is used by usethis to automatically manage
# roxygen namespace tags. Modify with care!
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