# HG changeset patch
# User greg
# Date 1517923475 18000
# Node ID 3b3001355f440a0c954756924c3e7bcfd1d1035c
# Parent  55d264cd49e8513520bdf2dad60d58ca0f642483
Uploaded

diff -r 55d264cd49e8 -r 3b3001355f44 ideas_preprocessor.R
--- a/ideas_preprocessor.R	Mon Feb 05 13:47:47 2018 -0500
+++ b/ideas_preprocessor.R	Tue Feb 06 08:24:35 2018 -0500
@@ -102,11 +102,17 @@
 to_path = paste(opt$output_files_path, "tmp.tar.gz", sep="/");
 file.rename("tmp.tar.gz", to_path);
 # Handle file names for display in the primary dataset if necessary.
-if (!is.null(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) {
-    # Renane opt$chrom_bed_input to be chromosomes.bed
-    # and make a copy of it in the output directory.
-    to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/");
+to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/");
+if (is.null(opt$chrom_bed_input) {
+    # Move cbi_file to the output directory,
+    # naming it chromosomes.bed.
+    file.rename(cbi_file, to_path);
+} else {
+    # Copy opt$chrom_bed_input to the output
+    # directory, naming it chromosomes.bed.
     file.copy(opt$chrom_bed_input, to_path);
+}
+if (!is.null(opt$chromosome_windows)) {
     # Move chromosome_windows.txt to the output directory.
     to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/");
     file.rename(opt$chromosome_windows, to_path);