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author | Daniel Baumann <daniel.baumann@progress-linux.org> | 2024-05-30 02:50:01 +0000 |
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committer | Daniel Baumann <daniel.baumann@progress-linux.org> | 2024-05-30 02:50:01 +0000 |
commit | 91275eb478ceb58083426099b6da3f4c7e189f19 (patch) | |
tree | 260f7d2fa77408b38c5cea96b320b9b0b6713ff2 /debian/vendor-h2o/deps/klib/ksw.h | |
parent | Merging upstream version 1.9.4. (diff) | |
download | dnsdist-91275eb478ceb58083426099b6da3f4c7e189f19.tar.xz dnsdist-91275eb478ceb58083426099b6da3f4c7e189f19.zip |
Merging debian version 1.9.4-1.
Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>
Diffstat (limited to 'debian/vendor-h2o/deps/klib/ksw.h')
-rw-r--r-- | debian/vendor-h2o/deps/klib/ksw.h | 72 |
1 files changed, 0 insertions, 72 deletions
diff --git a/debian/vendor-h2o/deps/klib/ksw.h b/debian/vendor-h2o/deps/klib/ksw.h deleted file mode 100644 index 5162dc0..0000000 --- a/debian/vendor-h2o/deps/klib/ksw.h +++ /dev/null @@ -1,72 +0,0 @@ -#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-dimention 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); - - 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); - 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); - -#ifdef __cplusplus -} -#endif - -#endif |