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#' get REF column from GRanges
#'
#' Retreives the REF column from a GRanges object.
#' This can be spelled as REF, Ref or ref.
#'
#' @param gr GRanges object
#'
#' @return DNAStringSet
#' @noRd
#'
.get_ref <- function(gr) {
gr_cols <- colnames(S4Vectors::mcols(gr))
if ("REF" %in% gr_cols) {
ref <- gr$REF
} else if ("ref" %in% gr_cols) {
ref <- gr$ref
} else if ("Ref" %in% gr_cols) {
ref <- gr$Ref
} else {
stop("Some of your data is missing a REF column.", call. = FALSE)
ref <- Biostrings::DNAStringSet()
}
return(ref)
}
#' get ALT column from GRanges
#'
#' Retreives the ALT column from a GRanges object.
#' This can be spelled as ALT, Alt or alt
#'
#' @param gr GRanges object
#'
#' @return DNAStringSetList
#' @noRd
#'
.get_alt <- function(gr) {
gr_cols <- colnames(S4Vectors::mcols(gr))
if ("ALT" %in% gr_cols) {
alt <- gr$ALT
} else if ("alt" %in% gr_cols) {
alt <- gr$alt
} else if ("Alt" %in% gr_cols) {
alt <- gr$Alt
} else {
stop("Some of your data is missing a ALT column.", call. = FALSE)
alt <- Biostrings::DNAStringSetList()
}
return(alt)
}
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