--- a/ideas_preprocessor.R	Wed Jan 24 14:04:47 2018 -0500
+++ b/ideas_preprocessor.R	Wed Jan 24 14:04:55 2018 -0500
@@ -1,11 +1,22 @@
 #!/usr/bin/env Rscript
 
+# TODO: implement support for the following:
+# 1. Scenario where user did not select chrom_bed_input
+# 2. --exclude_bed_input
+# 3. --bychr
+# 4. --chrom_len_file
+# 5. --reads_per_bp
+# 6. --restrict_to_chroms
+# 7. --standardize_datasets
+# 8. Scenario where --window_size is NULL and need to handle bamCoverage - see TODO near line # 57.
+
+
 suppressPackageStartupMessages(library("data.table"))
 suppressPackageStartupMessages(library("optparse"))
 
 option_list <- list(
         make_option(c("--chrom_bed_input"), action="store", dest="chrom_bed_input", defaul=NULL, help="Chromosome windows positions file"),
-        make_option(c("--exclude_input"), action="store", dest="exclude_input", defaul=NULL, help="File(s) containing regions to exclude"),
+        make_option(c("--exclude_bed_input"), action="store", dest="exclude_bed_input", defaul=NULL, help="File(s) containing regions to exclude"),
         make_option(c("--bychr"), action="store_true", dest="bychr", defaul=FALSE, help="Separate files by chromosome"),
         make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", default=NULL, help="Chromosome lengths file"),
         make_option(c("--ideaspre_input_config"), action="store", dest="ideaspre_input_config", help="Preprocessing input config file"),
@@ -42,8 +53,13 @@
 # Read the ideaspre_input_config text file which has this format:
 # "cell type name" "epigenetic factor name" "file path" "file name" "datatype"
 ideaspre_input_config = as.matrix(read.table(opt$ideaspre_input_config));
+
+# TODO: fix this
+window_size = opt$window_size
+if (is.null(opt$window_size)) {
+    window_size = 500;
+}
 # Process data to windows mean.
-# TODO: implement scenario where user did not select chrom_bed_input.
 if (!is.null(opt$chrom_bed_input)) {
     for (i in 1:dim(ideaspre_input_config)[1]) {
         file_path = ideaspre_input_config[i, 3]
@@ -53,7 +69,8 @@
             cmd = paste("samtools index", file_path);
             system(cmd);
             bigwig_file_name = paste(file_name, "bw", sep=".");
-            cmd = paste("bamCoverage --bam", file_path, "-o", bigwig_file_name, "--binSize", opt$window_size);
+
+            cmd = paste("bamCoverage --bam", file_path, "-o", bigwig_file_name, "--binSize", window_size);
             system(cmd);
         } else {
             bigwig_file_name = file_path;