--- a/ideas_preprocessor.R	Wed Jan 31 08:22:34 2018 -0500
+++ b/ideas_preprocessor.R	Wed Jan 31 08:22:43 2018 -0500
@@ -41,14 +41,10 @@
     for (i in 1:length(files)) {
         s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep="");
     }
-    s <- paste(s, '</ul>\n</body>\n</html>', sep="");
+    s <- paste(s, '</ul></body></html>', sep="");
     cat(s, file=output);
 }
 
-tmp_dir = "tmp";
-output_tmp_dir = paste(opt$output_files_path, tmp_dir, sep="/");
-dir.create(output_tmp_dir, showWarnings=FALSE);
-
 # Read the ideaspre_input_config text file which has this format:
 # "cell type name" "epigenetic factor name" "file path" "file name" "datatype"
 ideaspre_input_config = as.matrix(read.table(opt$ideaspre_input_config));
@@ -75,10 +71,9 @@
             bigwig_file_name = file_path;
         }
         bed_file_name = paste(file_name, "bed", sep=".");
-        bed_file_path = paste("tmp", bed_file_name, sep="/");
-        cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$chrom_bed_input, "stdout | cut -f5 >", bed_file_path);
+        cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$chrom_bed_input, "stdout | cut -f5 >", bed_file_name);
         system(cmd);
-        cmd = paste("gzip -f", bed_file_path);
+        cmd = paste("gzip -f", bed_file_name);
         system(cmd);
     }
 }
@@ -86,10 +81,8 @@
 # Create file1.txt.
 cmd = paste("cut -d' '", opt$ideaspre_input_config, "-f1,2 > file1.txt", sep=" ");
 system(cmd);
-# Compress the bed files in the tmp directory.
-tmp_gzipped_files = paste(tmp_dir, "*.bed.gz", sep="/");
-# Create file2.txt.
-cmd = paste("ls", tmp_gzipped_files, "> file2.txt", sep=" ");
+# Compress the bed files and create file2.txt.
+cmd = "ls *.bed.gz > file2.txt";
 system(cmd);
 # Create IDEAS_input_config.txt  with the format required by IDEAS.
 ideas_input_config = "IDEAS_input_config.txt"
@@ -98,14 +91,7 @@
 # Move IDEAS_input_config.txt to the output directory.
 to_path = paste(opt$output_files_path, ideas_input_config, sep="/");
 file.rename(ideas_input_config, to_path);
-# Move the compressed bed files in the tmp
-# directory to the output tmp directory.
-tmp_files = list.files(path=tmp_dir);
-for (i in 1:length(tmp_files)) {
-    from_path = paste(tmp_dir, tmp_files[i], sep="/");
-    to_path = paste(output_tmp_dir, tmp_files[i], sep="/");
-    file.rename(from_path, to_path);
-}
+# Handle optional chrom_bed_input.txt and chromosomes.bed files.
 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.