R/bed_random.r

In valr: Genome Interval Arithmetic

#' Generate randomly placed intervals on a genome.
#'
#' @param genome [genome_df]
#' @param length length of intervals
#' @param n number of intervals to generate
#' @param seed seed RNG for reproducible intervals
#' @param sorted return sorted output
#'
#' @details Sorting can be suppressed with `sorted = FALSE`.
#'
#' @return [ivl_df]
#'
#' @family randomizing operations
#'
#' @seealso \url{https://bedtools.readthedocs.io/en/latest/content/tools/random.html}
#'
#' @examples
#' genome <- tibble::tribble(
#'   ~chrom,  ~size,
#'   "chr1",  10000000,
#'   "chr2",  50000000,
#'   "chr3",  60000000,
#'   "chrX",  5000000
#' )
#'
#' bed_random(genome, seed = 10104)
#'
#' # sorting can be suppressed
#' bed_random(genome, sorted = FALSE, seed = 10104)
#'
#' # 500 random intervals of length 500
#' bed_random(genome, length = 500, n = 500, seed = 10104)
#'
#' @export
bed_random <- function(genome, length = 1000, n = 1e6, seed = 0, sorted = TRUE) {
  check_required(genome)

  genome <- check_genome(genome)

  if (!all(genome$size > length)) {
    cli::cli_abort("{.var length} must be smaller than all chrom sizes")
  }

  out <- random_impl(genome, length, n, seed)

  if (sorted) {
    out <- bed_sort(out)
  }

  as_tibble(out)
}