--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bntseq.h	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,80 @@
+/* The MIT License
+
+   Copyright (c) 2008 Genome Research Ltd (GRL).
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Contact: Heng Li <lh3@sanger.ac.uk> */
+
+#ifndef BWT_BNTSEQ_H
+#define BWT_BNTSEQ_H
+
+#include <stdint.h>
+#include <zlib.h>
+
+#ifndef BWA_UBYTE
+#define BWA_UBYTE
+typedef uint8_t ubyte_t;
+#endif
+
+typedef struct {
+	int64_t offset;
+	int32_t len;
+	int32_t n_ambs;
+	uint32_t gi;
+	char *name, *anno;
+} bntann1_t;
+
+typedef struct {
+	int64_t offset;
+	int32_t len;
+	char amb;
+} bntamb1_t;
+
+typedef struct {
+	int64_t l_pac;
+	int32_t n_seqs;
+	uint32_t seed;
+	bntann1_t *anns; // n_seqs elements
+	int32_t n_holes;
+	bntamb1_t *ambs; // n_holes elements
+	FILE *fp_pac;
+} bntseq_t;
+
+extern unsigned char nst_nt4_table[256];
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	void bns_dump(const bntseq_t *bns, const char *prefix);
+	bntseq_t *bns_restore(const char *prefix);
+	bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename);
+	void bns_destroy(bntseq_t *bns);
+	void bns_fasta2bntseq(gzFile fp_fa, const char *prefix);
+	int bns_coor_pac2real(const bntseq_t *bns, int64_t pac_coor, int len, int32_t *real_seq);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif