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- #ifndef __AC_KSW_H
- #define __AC_KSW_H
- #include <stdint.h>
- #define KSW_XBYTE 0x10000
- #define KSW_XSTOP 0x20000
- #define KSW_XSUBO 0x40000
- #define KSW_XSTART 0x80000
- struct _kswq_t;
- typedef struct _kswq_t kswq_t;
- typedef struct {
- int score; // best score
- int te, qe; // target end and query end
- int score2, te2; // second best score and ending position on the target
- int tb, qb; // target start and query start
- } kswr_t;
- #ifdef __cplusplus
- extern "C" {
- #endif
- /**
- * Aligning two sequences
- *
- * @param qlen length of the query sequence (typically <tlen)
- * @param query query sequence with 0 <= query[i] < m
- * @param tlen length of the target sequence
- * @param target target sequence
- * @param m number of residue types
- * @param mat m*m scoring matrix in one-dimension array
- * @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)"
- * @param gape gap extension penalty
- * @param xtra extra information (see below)
- * @param qry query profile (see below)
- *
- * @return alignment information in a struct; unset values to -1
- *
- * When xtra==0, ksw_align() uses a signed two-byte integer to store a
- * score and only finds the best score and the end positions. The 2nd best
- * score or the start positions are not attempted. The default behavior can
- * be tuned by setting KSW_X* flags:
- *
- * KSW_XBYTE: use an unsigned byte to store a score. If overflow occurs,
- * kswr_t::score will be set to 255
- *
- * KSW_XSUBO: track the 2nd best score and the ending position on the
- * target if the 2nd best is higher than (xtra&0xffff)
- *
- * KSW_XSTOP: stop if the maximum score is above (xtra&0xffff)
- *
- * KSW_XSTART: find the start positions
- *
- * When *qry==NULL, ksw_align() will compute and allocate the query profile
- * and when the function returns, *qry will point to the profile, which can
- * be deallocated simply by free(). If one query is aligned against multiple
- * target sequences, *qry should be set to NULL during the first call and
- * freed after the last call. Note that qry can equal 0. In this case, the
- * query profile will be deallocated in ksw_align().
- */
- kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry);
- kswr_t ksw_align2(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int xtra, kswq_t **qry);
- /**
- * Banded global alignment
- *
- * @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 free()
- *
- * @return score of the alignment
- */
- int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar, uint32_t **cigar);
- int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int *n_cigar, uint32_t **cigar);
- /**
- * Extend alignment
- *
- * The routine aligns $query and $target, assuming their upstream sequences,
- * which are not provided, have been aligned with score $h0. In return,
- * region [0,*qle) on the query and [0,*tle) on the target sequences are
- * aligned together. If *gscore>=0, *gscore keeps the best score such that
- * the entire query sequence is aligned; *gtle keeps the position on the
- * target where *gscore is achieved. Returning *gscore and *gtle helps the
- * caller to decide whether an end-to-end hit or a partial hit is preferred.
- *
- * The first 9 parameters are identical to those in ksw_global()
- *
- * @param h0 alignment score of upstream sequences
- * @param _qle (out) length of the query in the alignment
- * @param _tle (out) length of the target in the alignment
- * @param _gtle (out) length of the target if query is fully aligned
- * @param _gscore (out) score of the best end-to-end alignment; negative if not found
- *
- * @return best semi-local alignment score
- */
- int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off);
- int ksw_extend2(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int o_del, int e_del, int o_ins, int e_ins, int w, int end_bonus, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off);
- #ifdef __cplusplus
- }
- #endif
- #endif
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