Version tests

R/gen_tibble.R

@@ -288,9 +288,6 @@ gen_tibble.matrix <- function(x, indiv_meta, loci, ...,
     backingfile <- change_duplicated_file_name(backingfile)
   }
 
-  # use code for NA in FBM.256
-#  x[is.na(x)]<-3
-
   bigsnp_obj <- gt_write_bigsnp_from_dfs(genotypes = x,
                                           indiv_meta = indiv_meta,
                                           loci = loci,
@@ -383,7 +380,6 @@ gt_write_bigsnp_from_dfs <- function(genotypes, indiv_meta, loci,
                 sex = 0,
                 affection = 0,
                 ploidy = ploidy)
-
   map <- tibble(chromosome = loci$chromosome,
                 marker.ID = loci$name,
                 genetic.dist = as.double(loci$genetic_dist), ## make sure that genetic.dist is double
@@ -519,54 +515,38 @@ change_duplicated_file_name <- function(file){
   bk <- paste0(file, ".bk")
   rds <- paste0(file, ".rds")
 
-  if(file.exists(bk) && !file.exists(rds)){
-
+  if(file.exists(bk) | file.exists(rds)){
     version <- 2
-
-    base_name <- basename(file)
-
-    version_pattern <- paste0(base_name, "_v(\\d+)\\.bk$")
-
-    # read existing files to check for existing versions
-  existing_files <- list.files(dirname(bk), pattern = paste0("^", base_name, "_v\\d+\\.bk$"))
-
-
-    if (length(existing_files) > 0) {
-      versions <- sub(version_pattern, "\\1", existing_files)
-      versions <- as.numeric(versions)
-      if (!any(is.na(versions))) {
-        version <- max(versions) + 1
-      }
+    # extract the base name and version number
+    base_name_pattern <- "^(.*)_v(\\d+)$"
+    # check for any matches
+    matches <- regmatches(basename(file), regexec(base_name_pattern, basename(file)))
+
+    if (length(matches[[1]]) > 0) {
+      # Extract base name without version and current version number
+      base_name <- matches[[1]][2] # Part before "_v<number>"
+      current_version <- as.numeric(matches[[1]][3]) # extract current version number
+    } else {
+      base_name <- basename(file) # Use the full name if there's no "_v" suffix
+      current_version <- 1
     }
 
-    new_file <- paste0(file,"_v",version)
-
-    return(new_file)
-  } else if (file.exists(bk) && file.exists(rds)){
-
-    version <- 2
-
-    base_name <- basename(file)
-
     version_pattern <- paste0(base_name, "_v(\\d+)\\.bk$")
-
-    # read existing files to check for existing versions
+    # read files to check for existing versions
     existing_files <- list.files(dirname(bk), pattern = paste0("^", base_name, "_v\\d+\\.bk$"))
 
-
     if (length(existing_files) > 0) {
       versions <- sub(version_pattern, "\\1", existing_files)
       versions <- as.numeric(versions)
       if (!any(is.na(versions))) {
-        version <- max(versions) + 1
+        version <- max(versions) + 1 # add 1 to the version number
       }
     }
-
-    new_file <- paste0(file,"_v",version)
+    # create new file path
+    new_file <- paste0(dirname(file), "/", base_name, "_v", version)
 
     return(new_file)
   }
-
   return(file)
 
 }
@@ -579,6 +559,8 @@ cast_chromosome_to_int <- function(chromosome){
   }
   # if chromosome is a character, then cast it to integer
   if (is.character(chromosome)){
+    # attempt to strip chr from the chromosome
+    chromosome <- gsub("^(chromosome_|chr_|chromosome|chr)", "", chromosome, ignore.case = TRUE)
     chromosome <- tryCatch(as.integer(chromosome), warning = function(e) {as.integer(as.factor(chromosome))})
   }
   if (is.numeric(chromosome)){

R/gt_order_loci.R

@@ -11,20 +11,23 @@
 #' 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, quiet = FALSE, ...){
+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)
-  gt_update_backingfile(.x, quiet=quiet, ...)
+  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, ...)
 
 }

R/gt_update_backingfile.R

@@ -9,13 +9,16 @@
 #' for backing files used to store the data (they will be given a .bk
 #' and .RDS automatically). If left to NULL (the default), the file name
 #' will be based on the name f the current backing file.
+#' @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 chunk_size the number of loci to process at once
 #' @param quiet boolean to suppress information about the files
 #' @returns a [`gen_tibble`] with a backing file (i.e. a new File Backed Matrix)
 #' @export
 
 gt_update_backingfile <- function (.x, backingfile = NULL, chunk_size = NULL,
-                                    quiet = FALSE){
+                                    ignore_genetic_dist = TRUE, quiet = FALSE){
   # if the backingfile is null, create a name based on the current backing file
   if (is.null(backingfile)){
     backingfile <- change_duplicated_file_name(gt_get_file_names(.x)[2])
@@ -69,6 +72,18 @@
   # same for map
   map <- attr(.x$genotypes,"bigsnp")$map
   map <- map[.gt_bigsnp_cols(.x),]
+  # if we ignore genetic distance, set it to zero if it is not sorted
+  if (ignore_genetic_dist){
+    if (any(unlist(show_loci(.x) %>%
+                   group_by(.data$chr_int) %>%
+                   group_map(~ is.unsorted(.x$genetic_dist))))){
+      if (!quiet){
+        message("Genetic distances are not sorted, setting them to zero")
+      }
+      show_loci(.x)$genetic_dist <- 0
+    }
+  }
+
 
   # Create the bigSNP object
   bigsnp_obj <- structure(list(genotypes = new_bk_matrix, fam = fam, map = map),

R/is_loci_table_ordered.R

@@ -8,26 +8,28 @@
 #' or a [`gen_tibble`].
 #' @param error_on_false logical, if `TRUE` an error is thrown if the loci
 #' are not ordered.
+#' @param ignore_genetic_dist logical, if `TRUE` the physical position is not checked.
 #' @param ... other arguments passed to specific methods.
 #' @returns a logical vector defining which loci are transversions
 #' @rdname is_loci_table_ordered
 #' @export
-is_loci_table_ordered <- function(.x, error_on_false = FALSE, ...) {
+is_loci_table_ordered <- function(.x, error_on_false = FALSE, ignore_genetic_dist = TRUE, ...) {
   UseMethod("is_loci_table_ordered", .x)
 }
 
 #' @export
 #' @rdname is_loci_table_ordered
-is_loci_table_ordered.tbl_df <- function(.x, error_on_false = FALSE, ...) {
+is_loci_table_ordered.tbl_df <- function(.x, error_on_false = FALSE, ignore_genetic_dist = TRUE, ...) {
   #TODO this is a hack to deal with the class being dropped when going through group_map
   stopifnot_gen_tibble(.x)
-  is_loci_table_ordered(.x$genotypes, error_on_false, ...)
+  is_loci_table_ordered(.x$genotypes, error_on_false = error_on_false,
+                        ignore_genetic_dist = ignore_genetic_dist, ...)
 }
 
 
 #' @export
 #' @rdname is_loci_table_ordered
-is_loci_table_ordered.vctrs_bigSNP <- function(.x, error_on_false = FALSE, ...) {
+is_loci_table_ordered.vctrs_bigSNP <- function(.x, error_on_false = FALSE, ignore_genetic_dist = TRUE, ...) {
   rlang::check_dots_empty()
 
   # check that within each chromosome positions are sorted
@@ -49,6 +51,20 @@
       return(FALSE)
     }
   }
+
+  # check genetic distance
+  if (!ignore_genetic_dist){
+    if (any(unlist(show_loci(.x) %>%
+                   group_by(.data$chr_int) %>%
+                   group_map(~ is.unsorted(.x$genetic_dist))))){
+      if (error_on_false){
+        stop("Your genetic distances are not sorted within chromosomes")
+      } else {
+        return(FALSE)
+      }
+    }
+  }
+
   return(TRUE)
 }