--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtsw2.h	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,51 @@
+#ifndef LH3_BWTSW2_H
+#define LH3_BWTSW2_H
+
+#include <stdint.h>
+#include "bntseq.h"
+#include "bwt_lite.h"
+#include "bwt.h"
+
+typedef struct {
+	int a, b, q, r, t, qr, bw;
+	int z, is, t_seeds, hard_clip;
+	float yita, mask_level, coef;
+	int n_threads, chunk_size;
+} bsw2opt_t;
+
+typedef struct {
+	uint32_t k, l, flag:18, n_seeds:14;
+	int len, G, G2;
+	int beg, end;
+} bsw2hit_t;
+
+typedef struct {
+	int n, max;
+	bsw2hit_t *hits;
+	int *n_cigar;
+	uint32_t **cigar;
+} bwtsw2_t;
+
+typedef struct {
+	void *stack;
+	int max_l;
+	uint8_t *aln_mem;
+} bsw2global_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bsw2opt_t *bsw2_init_opt();
+	bwtsw2_t **bsw2_core(const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool);
+	void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target[2], const char *fn);
+	void bsw2_destroy(bwtsw2_t *b);
+
+	bsw2global_t *bsw2_global_init();
+	void bsw2_global_destroy(bsw2global_t *_pool);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif