Fails to grab RefSeq Genes for hg38

[cnobles]

Between hg18 and hg38, UCSC changed the track name from RefSeq Genes to NCBI RefSeq. This causes the script to fail when trying to pull the RefSeq genes data from UCSC and using hg38 as a reference. I have previously modified the "from_input" branch to use the below function, which can be found in the utils.R script.

getRefSeq_genes <- function(reference_genome) {
  # Identify table and track names
  bsession <- makeUCSCsession(reference_genome)
  trk_names <- names(trackNames(ucscTableQuery(bsession)))
  tbl_names <- tableNames(ucscTableQuery(bsession))

  trk <- grep("RefSeq", trk_names, value = TRUE)
  trk <- trk[trk %in% c("NCBI RefSeq", "RefSeq Genes")]
  stopifnot(length(trk) == 1)

  tbl <- grep("refGene", tbl_names, value = TRUE)
  stopifnot(length(tbl) == 1)

  refSeq <- makeGRanges(
    getUCSCtable(tbl, trk, freeze=reference_genome),
    freeze=reference_genome
  )
}