fixed ambiguous flags + nameing bug in find_kmer_regions

bin/reduce_bed.R

@@ -9,8 +9,8 @@ option_list <- list(
   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"),
-  make_option(opt_str = c("-mo", "--minoverlap_motif"), default = NULL, help = "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)", metavar = "integer", type = "integer"),
+  make_option(opt_str = c("-n", "--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"),
+  make_option(opt_str = c("-v", "--minoverlap_motif"), default = NULL, help = "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)", metavar = "integer", type = "integer"),
   make_option(opt_str = c("-f", "--motif_occurence"), default = 1, help = "Number of motifs per sequence any value above 0. Default = %default.", metavar = "double")
 )
 
@@ -196,14 +196,15 @@ find_kmer_regions <- function(bed, kmer_counts, minoverlap = 1 , threads = NULL)
 
   seq_ranges <- pbapply::pblapply(seq_len(nrow(bed)), cl = threads, function(x) {
     seq <- bed[x][[ncol(bed)]]
+    name <- bed[x][[4]]
 
     #### locate ranges
     ranges <- data.table::data.table(do.call(rbind, stringi::stri_locate_all_fixed(seq, pattern = kmer_counts[[1]])))
 
     ranges <- na.omit(ranges, cols = c("start", "end"))
 
     if (nrow(ranges) < 1) {
-      return(data.table::data.table(start = NA, end = NA, width = NA))
+      return(data.table::data.table(start = NA, end = NA, width = NA, name = name))
     }
 
     # add kmer sequences
@@ -237,14 +238,13 @@ find_kmer_regions <- function(bed, kmer_counts, minoverlap = 1 , threads = NULL)
     # reduce selected ranges
     reduced_ranges <- IRanges::reduce(reduced_ranges[selected_ranges])
 
-    reduced_ranges <- data.table::as.data.table(reduced_ranges)
+    reduced_ranges <- data.table::as.data.table(reduced_ranges)[, name := name]
 
     return(reduced_ranges)
   })
 
   # create ranges table
   conserved_regions_table <- data.table::rbindlist(seq_ranges)
-  conserved_regions_table[, name := bed[[4]]]
 
   return(conserved_regions_table)
 }