--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bwt_lite.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,94 @@
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include "bwt_lite.h"
+
+int is_sa(const uint8_t *T, uint32_t *SA, int n);
+int is_bwt(uint8_t *T, int n);
+
+bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq)
+{
+	bwtl_t *b;
+	int i;
+	b = (bwtl_t*)calloc(1, sizeof(bwtl_t));
+	b->seq_len = len;
+
+	{ // calculate b->bwt
+		uint8_t *s;
+		b->sa = (uint32_t*)calloc(len + 1, 4);
+		is_sa(seq, b->sa, len);
+		s = (uint8_t*)calloc(len + 1, 1);
+		for (i = 0; i <= len; ++i) {
+			if (b->sa[i] == 0) b->primary = i;
+			else s[i] = seq[b->sa[i] - 1];
+		}
+		for (i = b->primary; i < len; ++i) s[i] = s[i + 1];
+		b->bwt_size = (len + 15) / 16;
+		b->bwt = (uint32_t*)calloc(b->bwt_size, 4);
+		for (i = 0; i < len; ++i)
+			b->bwt[i>>4] |= s[i] << ((15 - (i&15)) << 1);
+		free(s);
+	}
+	{ // calculate b->occ
+		uint32_t c[4];
+		b->n_occ = (len + 15) / 16 * 4;
+		b->occ = (uint32_t*)calloc(b->n_occ, 4);
+		memset(c, 0, 16);
+		for (i = 0; i < len; ++i) {
+			if (i % 16 == 0)
+				memcpy(b->occ + (i/16) * 4, c, 16);
+			++c[bwtl_B0(b, i)];
+		}
+		memcpy(b->L2+1, c, 16);
+		for (i = 2; i < 5; ++i) b->L2[i] += b->L2[i-1];
+	}
+	{ // generate cnt_table
+		for (i = 0; i != 256; ++i) {
+			u_int32_t j, x = 0;
+			for (j = 0; j != 4; ++j)
+				x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
+			b->cnt_table[i] = x;
+		}
+	}
+	return b;
+}
+inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c)
+{
+	uint32_t n, b;
+	if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c];
+	if (k == (uint32_t)(-1)) return 0;
+	if (k >= bwt->primary) --k; // because $ is not in bwt
+	n = bwt->occ[k/16<<2|c];
+	b = bwt->bwt[k/16] & ~((1U<<((15-(k&15))<<1)) - 1);
+	n += (bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff]
+		  + bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24]) >> (c<<3) & 0xff;
+	if (c == 0) n -= 15 - (k&15); // corrected for the masked bits
+	return n;
+}
+inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
+{
+	uint32_t x, b;
+	if (k == (uint32_t)(-1)) {
+		memset(cnt, 0, 16);
+		return;
+	}
+	if (k >= bwt->primary) --k; // because $ is not in bwt
+	memcpy(cnt, bwt->occ + (k>>4<<2), 16);
+	b = bwt->bwt[k>>4] & ~((1U<<((~k&15)<<1)) - 1);
+	x = bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff]
+		+ bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24];
+	x -= 15 - (k&15);
+	cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
+}
+inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4])
+{
+	bwtl_occ4(bwt, k, cntk);
+	bwtl_occ4(bwt, l, cntl);
+}
+void bwtl_destroy(bwtl_t *bwt)
+{
+	if (bwt) {
+		free(bwt->occ); free(bwt->bwt); free(bwt->sa);
+		free(bwt);
+	}
+}