--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.7.9a/bwa.h	Thu Aug 14 02:16:48 2014 -0400
@@ -0,0 +1,50 @@
+#ifndef BWA_H_
+#define BWA_H_
+
+#include <stdint.h>
+#include "bntseq.h"
+#include "bwt.h"
+
+#define BWA_IDX_BWT 0x1
+#define BWA_IDX_BNS 0x2
+#define BWA_IDX_PAC 0x4
+#define BWA_IDX_ALL 0x7
+
+typedef struct {
+	bwt_t    *bwt; // FM-index
+	bntseq_t *bns; // information on the reference sequences
+	uint8_t  *pac; // the actual 2-bit encoded reference sequences with 'N' converted to a random base
+} bwaidx_t;
+
+typedef struct {
+	int l_seq;
+	char *name, *comment, *seq, *qual, *sam;
+} bseq1_t;
+
+extern int bwa_verbose;
+extern char bwa_rg_id[256];
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_);
+
+	void bwa_fill_scmat(int a, int b, int8_t mat[25]);
+	uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
+	uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
+
+	char *bwa_idx_infer_prefix(const char *hint);
+	bwt_t *bwa_idx_load_bwt(const char *hint);
+
+	bwaidx_t *bwa_idx_load(const char *hint, int which);
+	void bwa_idx_destroy(bwaidx_t *idx);
+
+	void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line);
+	char *bwa_set_rg(const char *s);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif