--- a/create_heatmap.R	Fri Nov 17 13:13:37 2017 -0500
+++ b/create_heatmap.R	Fri Nov 17 14:04:23 2017 -0500
@@ -111,11 +111,12 @@
 }
 
 # Read the inputs.
-para_files <- list.files(path=input_dir, pattern="*.para", full.names=TRUE);
-for (i in 1:length(para_files) {
+para_files <- list.files(path=opt$input_dir, pattern="\\.para$", full.names=TRUE);
+for (i in 1:length(para_files)) {
     para_file <- para_files[i];
-    para_file_base_name <- strsplit(para_file, ".para", fixed=TRUE)[1];
-    output_file_name <- paste(opt$output_dir, "/", para_file_base_name, ".pdf", sep="");
+    para_file_base_name <- strsplit(para_file, split="/")[[1]][2]
+    output_file_name <- gsub(".para", ".pdf", para_file_base_name)
+    output_file_path <- paste(opt$output_dir, "/", output_file_name, sep="");
     data_frame <- read.table(para_file, comment="!", header=T);
-    create_heatmap(data_frame, output_file_name);
+    create_heatmap(data_frame, output_file_path);
 }