renamed ignore_strand to strand

bin/cdhit_wrapper.R

@@ -24,7 +24,7 @@ option_list <- list(
   make_option(opt_str = c("-uS", "--max_unmatched_shorter_p"), default = 1.0, help = "Maximum unmatched percentage on shorter sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter)", metavar = "double"),
   make_option(opt_str = c("-U", "--max_unmatched_both_n"), default = 99999999, help = "Maximum unmatched nucleotied on both sequences (excludes leading tailing gap). Default = %default (CD-HIT parameter)", metavar = "integer"),
   make_option(opt_str = c("-g", "--fast_cluster"), default = 1, help = "Cluster sequence in first cluster that meets threshold = 0 (fast). Or cluster in best Cluster = 1 (accurate). Default = %default (CD-HIT parameter)", metavar = "integer"),
-  make_option(opt_str = c("-r", "--ignore_strand"), default = 0, help = "Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = %default (CD-HIT parameter)", metavar = "integer"),
+  make_option(opt_str = c("-r", "--strand"), default = 0, help = "Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = %default (CD-HIT parameter)", metavar = "integer"),
   make_option(opt_str = c("--match"), default = 2, help = "Matching score. Default = %default (CD-HIT parameter)", metavar = "integer"),
   make_option(opt_str = c("--mismatch"), default = -2, help = "Mismatch score. Default = %default (CD-HIT parameter)", metavar = "integer"),
   make_option(opt_str = c("--gap"), default = -6, help = "Gap score. Default = %default (CD-HIT parameter)", metavar = "integer"),
@@ -61,15 +61,15 @@ opt <- parse_args(opt_parser)
 #' @param max_unmatched_shorter_p Maximum unmatched percentage on shorter sequence (excludes leading tailing gap). Default = 1 (CD-HIT parameter)
 #' @param max_unmatched_both_n Maximum unmatched nucleotied on both sequences (excludes leading tailing gap). Default = 99999999 (CD-HIT parameter)
 #' @param fast_cluster Cluster sequence in first cluster that meets threshold = 0 (fast). Or cluster in best Cluster = 1 (accurate). Default = 1 (CD-HIT parameter)
-#' @param ignore_strand Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = 0 (CD-HIT parameter)
+#' @param strand Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = 0 (CD-HIT parameter)
 #' @param match Matching score. Default = 2 (CD-HIT parameter)
 #' @param mismatch Mismatch score. Default = -2 (CD-HIT parameter)
 #' @param gap Gap score. Default = -6 (CD-HIT parameter)
 #' @param gat_ext Gap extension score. Default = -1 (CD-HIT parameter)
 #' @param sort_cluster_by_size Either sort cluster by decreasing length (= 0) or by decreasing size (= 1). Default = 1 (CD-HIT parameter)
 #' 
 #' TODO check whether cdhit is installed
-cdhitest <- function(input, identity = 0.8, coverage = 8, output = "cluster.bed", clean = TRUE, threads = 1, global = 0, band_width = 20, memory = 800, word_length = 3, throw_away_sequences = 5, length_dif_cutoff_shorter_p = 0, length_dif_cutoff_shorter_n = 999999, alignment_coverage_longer_p = 0, alignment_coverage_longer_n = 99999999, alignment_coverage_shorter_p = 0, alignment_coverage_shorter_n = 99999999, max_unmatched_longer_p = 1, max_unmatched_shorter_p = 1, max_unmatched_both_n = 99999999, fast_cluster = 1, ignore_strand = 0, match = 2, mismatch = -2, gap = -6, gap_ext = -1, sort_cluster_by_size = 1) {
+cdhitest <- function(input, identity = 0.8, coverage = 8, output = "cluster.bed", clean = TRUE, threads = 1, global = 0, band_width = 20, memory = 800, word_length = 3, throw_away_sequences = 5, length_dif_cutoff_shorter_p = 0, length_dif_cutoff_shorter_n = 999999, alignment_coverage_longer_p = 0, alignment_coverage_longer_n = 99999999, alignment_coverage_shorter_p = 0, alignment_coverage_shorter_n = 99999999, max_unmatched_longer_p = 1, max_unmatched_shorter_p = 1, max_unmatched_both_n = 99999999, fast_cluster = 1, strand = 0, match = 2, mismatch = -2, gap = -6, gap_ext = -1, sort_cluster_by_size = 1) {
   if (missing(input)) {
     stop("Input parameter missing!")
   }
@@ -118,7 +118,7 @@ cdhitest <- function(input, identity = 0.8, coverage = 8, output = "cluster.bed"
                       "-uS", max_unmatched_shorter_p,
                       "-U", max_unmatched_both_n,
                       "-g", fast_cluster,
-                      "-r", ignore_strand,
+                      "-r", strand,
                       "-match", match,
                       "-mismatch", mismatch,
                       "-gap", gap,