--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction/src/main.cpp	Sun Feb 21 23:31:55 2016 -0500
@@ -0,0 +1,37 @@
+#include <string>
+#include <iostream>
+#include <vector>
+
+#include "int_util.h"
+#include "dir_util.h"
+#include "args.h"
+#include "Fasta.h"
+#include "Sam.h"
+#include "SamRatio.h"
+
+using namespace std;
+
+int main(int argc, char *argv[]) {
+	cmd_args args;
+	args = parse_command_line(argc, argv);
+
+	Fasta f(args.amr_fp);
+	f.read_fasta(args.amr_fp);	
+
+	if(args.sam_dir) {
+		list<string> sam_files = parse_sam_dir(args.sam_fp);
+		for(auto &fn : sam_files) {
+			args.sam_fp = fn;
+			Sam s(args.sam_fp);
+			s.read_sam(args);
+			generate_samples(f.records, s.alignment, args);
+		}
+	}
+	else {
+		Sam s(args.sam_fp);
+		s.read_sam(args);
+		generate_samples(f.records, s.alignment, args);
+	}
+
+	return 0;
+}