--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/tools/read_utils/get_reads_direct.h	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,23 @@
+/* written by Jonas Behr, Regina Bohnert and Gunnar Raetsch, FML Tuebingen, Germany, 2010 */
+
+#ifndef __GET_READS_DIRECT_H__
+#define __GET_READS_DIRECT_H__
+
+#include <vector>
+  using std::vector;
+#include "read.h"
+#include <stdlib.h>
+#include "sam.h"
+
+//static int g_flag_on = 0, g_flag_off = 0;
+static int left_flag_mask = strtol((char*) "0x40", 0, 0);
+static int right_flag_mask = strtol((char*) "0x80", 0, 0);
+static int reverse_flag_mask = strtol((char*) "0x10", 0, 0);
+
+static int subsample = 1000; 
+//static int collapse = 0;
+
+int get_reads_from_bam(char* filename, char* region, vector<CRead*>* reads, char strand, int lsubsample);
+void parse_cigar(bam1_t* b, CRead* read, bam_header_t* header);
+
+#endif