to replace

ksw2.h

@@ -1,38 +0,0 @@
-#ifndef KSW2_H_
-#define KSW2_H_
-
-#include <stdint.h>
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/**
- * Global alignment with moving a band
- *
- * @param km        memory pool, when used with kalloc
- * @param qlen      query length
- * @param query     query sequence with 0 <= query[i] < m
- * @param tlen      target length
- * @param target    target sequence with 0 <= target[i] < m
- * @param m         number of residue types
- * @param mat       m*m scoring mattrix in one-dimension array
- * @param gapo      gap open penalty; a gap of length l cost "-(gapo+l*gape)"
- * @param gape      gap extension penalty
- * @param w         band width
- * @param n_cigar   (out) number of CIGAR elements
- * @param cigar     (out) BAM-encoded CIGAR; caller need to deallocate with kfree(km, )
- *
- * @return          score of the alignment
- */
-int ksw_global(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_);
-int ksw_global2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_);
-int ksw_global2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_);
-
-void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif