R/nucmerToPaf.R

In daewoooo/SVbyEye: Visualization of genomic structural variants

#' Read nucmer coordinates file in to PAF formatted table
#'
#' This function takes alignments produced by nucmer (parameters: --mum --coords) and loads
#' reported coordinates file (suffix .coords) into a PAF formatted table (see PAF specification).
#'
#' @param nucmer.coords A path to a nucmer coordinates file containing alignments to be loaded.
#' @importFrom utils read.table
#' @importFrom tibble tibble
#' @return A \code{tibble} of PAF formatted table
#' @author David Porubsky
#' @export
#' @examples
#' ## Get nucmer coordinates to read in ##
#' nucmer.coords <- system.file("extdata", "HG00438_1_nucmer.coords", package = "SVbyEye")
#' ## Read in nucmer coordinates
#' nucmer2PAF(nucmer.coords = nucmer.coords)
#'
nucmer2PAF <- function(nucmer.coords = NULL) {
    ## Check is path to nucmer coordinates has been defined and if the file exists
    if (!is.null(nucmer.coords)) {
        if (file.exists(nucmer.coords)) {
            ## Read in coordinates from nucmer output
            coords <- utils::read.table(nucmer.coords, skip = 5, stringsAsFactors = FALSE)
            coords.tb <- tibble::tibble(
                q.name = coords$V12,
                q.len = max(c(coords$V1, coords$V2)),
                q.start = coords$V1,
                q.end = coords$V2,
                strand = ifelse(coords$V4 < coords$V5, "+", "-"),
                t.name = coords$V13,
                t.len = max(c(coords$V4, coords$V5)),
                t.start = pmin(coords$V4, coords$V5),
                t.end = pmax(coords$V4, coords$V5),
                n.match = coords$V10,
                aln.len = coords$V8,
                mapq = NA
            )
        } else {
            coords.tb <- NULL
        }
        return(coords.tb)
    }
}