gt_order_loci.R

#' Order the loci table of a gen_tibble
#'
#' This function reorders the loci table so that positions within a chromosome
#' are sequential. It also re-saves the genotypes into a new file backed matrix
#' with the new order, so that it can be used by functions such as [loci_ld_clump()]
#' and [gt_pca_autoSVD()]. If the loci table is already ordered, the original
#' `gen_tibble` is returned.
#'
#' @param .x a [`gen_tibble`]
#' @param use_current_table boolean, if FALSE (the default), the table will be
#' reordered; if TRUE, then the current loci table, which might have been reordered
#' manually, will be used, but only if the positions within each chromosome are
#' sequential
#' @param ignore_genetic_dist boolean to ignore the genetic distance when checking. Note
#' that, if `gentic_dist` are being ignored and they are not sorted, the function will
#' set them to zero to avoid problems with other software.
#' @param quiet boolean to suppress information about the files
#' @param ... other arguments
#' @return A [gen_tibble]
#' @export

gt_order_loci <- function(.x, use_current_table = FALSE, ignore_genetic_dist = TRUE, quiet = FALSE, ...){
  if (use_current_table){
    new_table <- show_loci(.x)
  } else {
    new_table <- show_loci(.x) %>% dplyr::arrange(.data$chr_int, .data$position)
    show_loci(.x) <- new_table
  }
  # if asked to use the current table, check that it is ordered
  is_loci_table_ordered(.x, error_on_false = TRUE, ignore_genetic_dist = ignore_genetic_dist)
  gt_update_backingfile(.x, quiet=quiet, ignore_genetic_dist = ignore_genetic_dist, ...)

}