threads = 0 for all cores to match cd-hit

bin/reduce_bed.R

@@ -6,7 +6,7 @@ option_list <- list(
   make_option(opt_str = c("-k", "--kmer"), default = 10, help = "Kmer length. Default = %default", metavar = "integer"),
   make_option(opt_str = c("-m", "--motif"), default = 10, help = "Estimated motif length. Default = %default", metavar = "integer"),
   make_option(opt_str = c("-o", "--output"), default = "reduced.bed", help = "Output file. Default = %default", metavar = "character"),
-  make_option(opt_str = c("-t", "--threads"), default = 1, help = "Number of threads to use. Use -1 for all available cores. Default = %default", metavar = "integer"),
+  make_option(opt_str = c("-t", "--threads"), default = 1, help = "Number of threads to use. Use 0 for all available cores. Default = %default", metavar = "integer"),
   make_option(opt_str = c("-c", "--clean"), default = TRUE, help = "Delete all temporary files. Default = %default", metavar = "logical"),
   make_option(opt_str = c("-s", "--min_seq_length"), default = NULL, help = "Remove sequences below this length. Defaults to the maximum value of motif and kmer and can not be lower.", metavar = "integer", type = "integer"),
   make_option(opt_str = c("-ko", "--minoverlap_kmer"), default = NULL, help = "Minimum required overlap between kmer to merge kmer. Used to create reduced sequence ranges. Can not be greater than kmer length. Default = kmer - 1", metavar = "integer", type = "integer"),
@@ -25,7 +25,7 @@ opt <- parse_args(opt_parser)
 #' @param kmer Length of kmer.
 #' @param motif Estimated motif length.
 #' @param output Output file
-#' @param threads Number of threads.
+#' @param threads Number of threads. Default = 1. 0 for all cores.
 #' @param clean Delete all temporary files.
 #' @param minoverlap_kmer Minimum required overlap between kmer to merge kmer. Used to create reduced sequence ranges. Can not be greater than kmer length. Default = kmer - 1
 #' @param minoverlap_motif Minimum required overlap between motif and kmer to consider kmer significant. Used for kmer cutoff calculation. Can not be greater than motif and kmer length. Default = ceiling(motif / 2)
@@ -36,7 +36,7 @@ opt <- parse_args(opt_parser)
 #' TODO check whether jellyfish is installed
 reduce_bed <- function(input, kmer = 10, motif = 10, output = "reduced.bed", threads = NULL, clean = TRUE, minoverlap_kmer = kmer - 1, minoverlap_motif = ceiling(motif / 2), min_seq_length = max(c(motif, kmer)), motif_occurence = 1) {
   # get number of available cores
-  if (threads == -1) {
+  if (threads == 0) {
     threads <- parallel::detectCores()
   }