--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bwase.h~	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,27 @@
+#ifndef BWASE_H
+#define BWASE_H
+
+#include "bntseq.h"
+#include "bwt.h"
+#include "bwtaln.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	// Initialize mapping tables in the bwa single-end mapper.
+	void bwase_initialize();
+	// Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
+	void bwa_cal_pac_pos_core(const bwt_t* forward_bwt, const bwt_t* reverse_bwt, bwa_seq_t* seq, const int max_mm, const float fnr);
+	// Refine the approximate position of the sequence to an actual placement for the sequence.
+	void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns);
+	// Backfill certain alignment properties mainly centering around number of matches.
+	void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
+	// Calculate the end position of a read given a certain sequence.
+	int64_t pos_end(const bwa_seq_t *p);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif // BWASE_H