R/bed_complement.r

In valr: Genome Interval Arithmetic

#' Identify intervals in a genome not covered by a query.
#'
#' @param x [ivl_df]
#' @param genome [ivl_df]
#'
#' @family single set operations
#'
#' @return [ivl_df]
#'
#' @examples
#' x <- tibble::tribble(
#'   ~chrom, ~start, ~end,
#'   "chr1", 0,      10,
#'   "chr1", 75,     100
#' )
#'
#' genome <- tibble::tribble(
#'   ~chrom, ~size,
#'   "chr1", 200
#' )
#'
#' bed_glyph(bed_complement(x, genome))
#'
#' genome <- tibble::tribble(
#'   ~chrom,  ~size,
#'   "chr1",  500,
#'   "chr2",  600,
#'   "chr3",  800
#' )
#'
#' x <- tibble::tribble(
#'   ~chrom, ~start, ~end,
#'   "chr1", 100,    300,
#'   "chr1", 200,    400,
#'   "chr2", 0,      100,
#'   "chr2", 200,    400,
#'   "chr3", 500,    600
#' )
#'
#' # intervals not covered by x
#' bed_complement(x, genome)
#'
#' @export
bed_complement <- function(x, genome) {
  check_required(x)
  check_required(genome)

  x <- check_interval(x)
  genome <- check_genome(genome)

  res <- bed_merge(x)

  # non-overlapping chroms
  chroms_no_overlaps <- anti_join(genome, res, by = "chrom")
  chroms_no_overlaps <- mutate(chroms_no_overlaps, start = 0)
  chroms_no_overlaps <- select(chroms_no_overlaps, chrom, start, end = size)

  # remove rows from x that are not in genome
  res <- semi_join(res, genome, by = "chrom")

  res <- group_by(res, chrom)

  res <- complement_impl(res, genome)

  res <- bind_rows(res, as_tibble(chroms_no_overlaps))
  res <- bed_sort(res)

  res
}