--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bwt.h	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,105 @@
+/* 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 BWA_BWT_H
+#define BWA_BWT_H
+
+#include <stdint.h>
+
+// requirement: (OCC_INTERVAL%16 == 0)
+#define OCC_INTERVAL 0x80
+
+#ifndef BWA_UBYTE
+#define BWA_UBYTE
+typedef unsigned char ubyte_t;
+#endif
+typedef uint32_t bwtint_t;
+
+typedef struct {
+	bwtint_t primary; // S^{-1}(0), or the primary index of BWT
+	bwtint_t L2[5]; // C(), cumulative count
+	bwtint_t seq_len; // sequence length
+	bwtint_t bwt_size; // size of bwt, about seq_len/4
+	uint32_t *bwt; // BWT
+	// occurance array, separated to two parts
+	uint32_t cnt_table[256];
+	// suffix array
+	int sa_intv;
+	bwtint_t n_sa;
+	bwtint_t *sa;
+} bwt_t;
+
+#define bwt_bwt(b, k) ((b)->bwt[(k)/OCC_INTERVAL*12 + 4 + (k)%OCC_INTERVAL/16])
+
+/* retrieve a character from the $-removed BWT string. Note that
+ * bwt_t::bwt is not exactly the BWT string and therefore this macro is
+ * called bwt_B0 instead of bwt_B */
+#define bwt_B0(b, k) (bwt_bwt(b, k)>>((~(k)&0xf)<<1)&3)
+
+#define bwt_occ_intv(b, k) ((b)->bwt + (k)/OCC_INTERVAL*12)
+
+// inverse Psi function
+#define bwt_invPsi(bwt, k)												\
+	(((k) == (bwt)->primary)? 0 :										\
+	 ((k) < (bwt)->primary)?											\
+	 (bwt)->L2[bwt_B0(bwt, k)] + bwt_occ(bwt, k, bwt_B0(bwt, k))		\
+	 : (bwt)->L2[bwt_B0(bwt, (k)-1)] + bwt_occ(bwt, k, bwt_B0(bwt, (k)-1)))
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	void bwt_dump_bwt(const char *fn, const bwt_t *bwt);
+	void bwt_dump_sa(const char *fn, const bwt_t *bwt);
+
+	bwt_t *bwt_restore_bwt(const char *fn);
+	void bwt_restore_sa(const char *fn, bwt_t *bwt);
+
+	void bwt_destroy(bwt_t *bwt);
+
+	void bwt_bwtgen(const char *fn_pac, const char *fn_bwt); // from BWT-SW
+	void bwt_cal_sa(bwt_t *bwt, int intv);
+
+	void bwt_bwtupdate_core(bwt_t *bwt);
+
+	inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
+	inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
+	bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k);
+
+	// more efficient version of bwt_occ/bwt_occ4 for retrieving two close Occ values
+	void bwt_gen_cnt_table(bwt_t *bwt);
+	inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
+	inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);
+
+	int bwt_match_exact(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *sa_begin, bwtint_t *sa_end);
+	int bwt_match_exact_alt(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *k0, bwtint_t *l0);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif