--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction/src/dir_util.h	Sun Feb 21 23:31:55 2016 -0500
@@ -0,0 +1,43 @@
+#ifndef DIR_UTIL_H
+#define DIR_UTIL_H
+
+#include <list>
+#include <iostream>
+#include <string>
+#include <dirent.h>
+
+/*
+ * Parses a directory of sam files
+ */
+static inline std::list<std::string>
+parse_sam_dir(const std::string &directory) {
+        DIR *dir;
+        struct dirent *ent;
+        std::string dir_path = directory;
+
+        dir = opendir(dir_path.c_str());
+	// is dir open/valid?
+        if(dir == NULL) {
+                std::cout << "Not a valid directory" << std::endl;
+                exit(EXIT_FAILURE);
+        }
+
+        std::list<std::string> sam_files;
+        std::string fn;
+        std::string ext;
+        std::string file_type = ".sam";
+
+	// get all files with a .sam file extension
+        while((ent = readdir(dir)) != NULL) {
+                fn = dir_path + std::string(ent->d_name);
+                ext = fn.substr(fn.length()-4, fn.length());
+                if(ext.compare(file_type) == 0) {
+                        sam_files.push_back(fn);
+                }
+        }
+        closedir(dir);
+
+        return sam_files;
+}
+
+#endif /* DIR_UTIL_H */