--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mrcanavar-0.34/sam.h	Tue Feb 21 10:44:13 2012 -0500
@@ -0,0 +1,28 @@
+#ifndef __SAM
+#define __SAM
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <dirent.h>
+
+#include "globals.h"
+#include "utils.h"
+
+void read_depth(char *, char *, char);
+void readSAM(char *, char *, char);
+
+int insert_read_lw(char *, int, char *, int);
+int insert_read_sw(char *, int, char *, int);
+int insert_read_cw(char *, int, char *, int);
+
+int findChrom(char *, char *, int);
+
+int binSearch(char *);
+
+int windowSearch(struct window *, int, int);
+
+void saveDepth(char *);
+
+#endif