inst/R_cli/vcf_cleaning.R

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

#' #' Remove old vcf files
#' #'
#' #' @keywords internal
#' vcf_cleaning <- function(root = ".",
#'                          LD_ref = "1KGphase3",
#'                          loci = NULL,
#'                          verbose = TRUE) {
#'     files <- list.files(root, paste0("*", LD_ref, ".vcf.gz|.vcf.gz.tbi", "*"),
#'         recursive = TRUE, full.names = TRUE
#'     )
#' 
#'     if (!is.null(loci)) {
#'         locus_names <- unique(basename(dirname(dirname(files))))
#'         select_loci <- dplyr::intersect(loci, locus_names)
#'         if (length(select_loci) > 0) {
#'             files <- files[locus_names %in% select_loci]
#'         }
#'     }
#'     if (length(files) > 0) {
#'         messager("Removing", length(files), "files.", v = verbose)
#'         out <- file.remove(files)
#'     }
#' }