#' Get CpG islands annotations
 #'
 #' Helper functions are provided for obtaining CpG islands annotations from UCSC table browser.
 #'

 #' @keywords internal

 #'
 #' @return tibble (data.frame) object containing CpG islands annotation.
 #'
 get_cgi <- function(genome) {

     available_genomes <- c("hg19", "hg38", "mm10", "grcm39")

     assertthat::assert_that(
         genome %in% available_genomes,
         msg = sprintf("genome must be one of %s", paste(available_genomes, collapse = ", "))
     )
 
     rds_path <- switch(
         genome,
         hg19 = system.file("cgi_hg19.rds", package = "NanoMethViz"),
         hg38 = system.file("cgi_hg38.rds", package = "NanoMethViz"),
         mm10 = system.file("cgi_mm10.rds", package = "NanoMethViz"),

         grcm39 = system.file("cgi_GRCm39.rds", package = "NanoMethViz")

     )
 
     readRDS(rds_path)
 }
 
 #' @rdname get_exons
 #'
 #' @examples
 #' cgi_mm10 <- get_cgi_mm10()
 #'
 #' @export
 get_cgi_mm10 <- function() {
     get_cgi("mm10")
 }
 
 #' @rdname get_exons
 #'
 #' @examples

 #' cgi_GRCm39 <- get_cgi_grcm39()

 #'
 #' @export

 get_cgi_grcm39 <- function() {
     get_cgi("grcm39")

 }
 
 #' @rdname get_exons
 #'
 #' @examples
 #' cgi_hg19 <- get_cgi_hg19()
 #'
 #' @export
 get_cgi_hg19 <- function() {
     get_cgi("hg19")
 }
 
 #' @rdname get_exons
 #'
 #' @examples
 #' cgi_hg38 <- get_cgi_hg38()
 #'
 #' @export
 get_cgi_hg38 <- function() {
     get_cgi("hg38")
 }