When 'replace = FALSE' is set in

extract_random_seqs_from_genome(), the command will still hold 'replace = TRUE' for the chromosome and strand to be sampled, but the sequence that
was sampled will be removed #2

R/extract_random_seqs_from_genome.R

@@ -79,15 +79,17 @@ extract_random_seqs_from_genome <-
         res <- vector("list", length(size))
 
         for (i in seq_len(size)) {
-          sample_chromsome <- sample.int(length(chr_names), 1, replace = replace, prob = prob)
+          sample_chromsome <- sample.int(length(chr_names), 1, replace = TRUE, prob = NULL)
           sample_strand <- sample.int(2, 1, replace = replace, prob = c(0.5, 0.5))
 
           if (sample_strand == 1){
             sample_i <- sample_chromosome_intervals(
               chr_size = imported_genome_i[chr_names[sample_chromsome]]@ranges@width,
               interval_width = interval_width,
               strand = "plus",
-              size = 1
+              size = 1,
+              replace = replace,
+              prob = prob
             )
 
             sample_i <- dplyr::mutate(sample_i, chr = chr_names[sample_chromsome])
@@ -99,7 +101,9 @@ extract_random_seqs_from_genome <-
               chr_size = imported_genome_i[chr_names[sample_chromsome]]@ranges@width,
               interval_width = interval_width,
               strand = "minus",
-              size = 1
+              size = 1,
+              replace = replace,
+              prob = prob
             )
 
                 sample_i <-

R/sample_chromosome_intervals.R

@@ -10,9 +10,17 @@
 #' \item \code{strand = "minus"}
 #' }
 #' @param size a non-negative integer giving the number of sequences that shall be sampled from random genomic loci.
+#' @param replace logical value indicating whether sampling should be with replacement. Default: \code{replace = TRUE}.
+#' @param prob a vector of probability weights for obtaining the elements of the vector being sampled. Default is \code{prob = NULL}.
 #' @author Hajk-Georg Drost
-sample_chromosome_intervals <- function(chr_size, interval_width, strand, size) {
-
+sample_chromosome_intervals <-
+  function(chr_size,
+           interval_width,
+           strand,
+           size,
+           replace = TRUE,
+           prob = NULL) {
+
   if (!is.element(strand, c("plus", "minus")))
     stop("The 'strand' argument can only be specified as strand = 'plus' or strand = 'minus'.", call. = FALSE)
 
@@ -27,7 +35,11 @@ sample_chromosome_intervals <- function(chr_size, interval_width, strand, size)
     }
 
   # random start position in chromosome
-  random_start <- sample.int(ifelse((chr_size - interval_width) == 0,1, chr_size - interval_width), size)
+    random_start <-
+      sample.int(ifelse((chr_size - interval_width) == 0, 1, chr_size - interval_width),
+                 size,
+                 replace = replace,
+                 prob = prob)
   # compute random end position in chromosome given interval width
   random_end <- random_start + interval_width - 1