diff bwa-0.6.2/bwt_lite.h @ 2:a294fbfcb1db draft default tip

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/bwt_lite.h	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,29 @@
+#ifndef BWT_LITE_H_
+#define BWT_LITE_H_
+
+#include <stdint.h>
+
+typedef struct {
+	uint32_t seq_len, bwt_size, n_occ;
+	uint32_t primary;
+	uint32_t *bwt, *occ, *sa, L2[5];
+	uint32_t cnt_table[256];
+} bwtl_t;
+
+#define bwtl_B0(b, k) ((b)->bwt[(k)>>4]>>((~(k)&0xf)<<1)&3)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq);
+	inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
+	inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
+	inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
+	void bwtl_destroy(bwtl_t *bwt);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif