mirror of
https://github.com/attractivechaos/klib
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73 lines
2.7 KiB
C
73 lines
2.7 KiB
C
#ifndef __AC_KSW_H
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#define __AC_KSW_H
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#include <stdint.h>
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#define KSW_XBYTE 0x10000
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#define KSW_XSTOP 0x20000
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#define KSW_XSUBO 0x40000
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#define KSW_XSTART 0x80000
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struct _kswq_t;
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typedef struct _kswq_t kswq_t;
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typedef struct {
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int score; // best score
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int te, qe; // target end and query end
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int score2, te2; // second best score and ending position on the target
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int tb, qb; // target start and query start
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} kswr_t;
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#ifdef __cplusplus
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extern "C" {
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#endif
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/**
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* Aligning two sequences
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*
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* @param qlen length of the query sequence (typically <tlen)
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* @param query query sequence with 0 <= query[i] < m
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* @param tlen length of the target sequence
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* @param target target sequence
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* @param m number of residue types
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* @param mat m*m scoring matrix in one-dimention array
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* @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)"
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* @param gape gap extension penalty
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* @param xtra extra information (see below)
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* @param qry query profile (see below)
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*
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* @return alignment information in a struct; unset values to -1
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*
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* When xtra==0, ksw_align() uses a signed two-byte integer to store a
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* score and only finds the best score and the end positions. The 2nd best
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* score or the start positions are not attempted. The default behavior can
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* be tuned by setting KSW_X* flags:
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*
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* KSW_XBYTE: use an unsigned byte to store a score. If overflow occurs,
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* kswr_t::score will be set to 255
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*
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* KSW_XSUBO: track the 2nd best score and the ending position on the
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* target if the 2nd best is higher than (xtra&0xffff)
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*
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* KSW_XSTOP: stop if the maximum score is above (xtra&0xffff)
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*
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* KSW_XSTART: find the start positions
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*
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* When *qry==NULL, ksw_align() will compute and allocate the query profile
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* and when the function returns, *qry will point to the profile, which can
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* be deallocated simply by free(). If one query is aligned against multiple
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* target sequences, *qry should be set to NULL during the first call and
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* freed after the last call. Note that qry can equal 0. In this case, the
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* query profile will be deallocated in ksw_align().
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*/
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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);
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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 h0, int *_qle, int *_tle);
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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);
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#ifdef __cplusplus
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}
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#endif
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#endif
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