implemented minoverlap_kmer & minoverlap_motif

bin/reduce_bed.R

@@ -8,7 +8,9 @@ option_list <- list(
   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("-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("-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")
   # TODO more args
 )
 
@@ -25,13 +27,13 @@ opt <- parse_args(opt_parser)
 #' @param output Output file
 #' @param threads Number of threads.
 #' @param clean Delete all temporary files.
-#' @param minoverlap_kmer Minimum required overlap between kmer to merge kmer. Used to create reduced sequence ranges.# TODO
-#' @param minoverlap_motif Minimum required overlap between motif and kmer to consider kmer significant. Used for kmer cutoff calculation.# TODO
+#' @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)
 #' @param min_seq_length Must be greater or equal to kmer and motif. Default = max(c(motif, kmer)).
 #' 
 #' @return reduced bed
 #' TODO check whether jellyfish is installed
-reduce_bed <- function(input, kmer = 10, motif = 10, output = "reduced.bed", threads = NULL, clean = TRUE, minoverlap_kmer, minoverlap_motif, min_seq_length = max(c(motif, kmer))) {
+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))) {
   # get number of available cores
   if (threads == -1) {
     threads <- parallel::detectCores()
@@ -91,16 +93,16 @@ reduce_bed <- function(input, kmer = 10, motif = 10, output = "reduced.bed", thr
   data.table::setorder(kmer_counts, -V2)
 
   # compute number of hits to keep
-  keep_hits <- significant_kmer(bed_table, kmer = kmer, motif = motif)
+  keep_hits <- significant_kmer(bed_table, kmer = kmer, motif = motif, minoverlap = minoverlap_motif)
 
   # reduce kmer
-  reduced_kmer <- reduce_kmer(kmer = kmer_counts, keep_hits)
+  reduced_kmer <- reduce_kmer(kmer = kmer_counts, significant = keep_hits)
 
   message("Find kmer in sequences.")
   # find k-mer in sequences
   # TODO minoverlap as parameter
   # columns: name, start, end, width
-  ranges_table <- find_kmer_regions(bed = bed_table, kmer_counts = reduced_kmer, minoverlap = kmer - 1, threads = threads)
+  ranges_table <- find_kmer_regions(bed = bed_table, kmer_counts = reduced_kmer, minoverlap = minoverlap_kmer, threads = threads)
   names(ranges_table)[1:2] <- c("relative_start", "relative_end")
 
   # merge ranged_table with bed_table + keep column order
@@ -139,7 +141,7 @@ reduce_bed <- function(input, kmer = 10, motif = 10, output = "reduced.bed", thr
 #' @return Number of interesting kmer.
 significant_kmer <- function(bed, kmer, motif, minoverlap = ceiling(motif / 2)) {
   if (minoverlap > kmer || minoverlap > motif) {
-    stop("Kmer & motif must be greater or equal than minoverlap!")
+    stop("Kmer & motif must be greater or equal to minoverlap!")
   }
 
   # minimum sequence length to get all interesting overlaps