c_cpp/lib/klib/ksw.h

   1 #ifndef __AC_KSW_H
   2 #define __AC_KSW_H
   3
   4 #include <stdint.h>
   5
   6 #define KSW_XBYTE  0x10000
   7 #define KSW_XSTOP  0x20000
   8 #define KSW_XSUBO  0x40000
   9 #define KSW_XSTART 0x80000
  10
  11 struct _kswq_t;
  12 typedef struct _kswq_t kswq_t;
  13
  14 typedef struct {
  15         int score; // best score
  16         int te, qe; // target end and query end
  17         int score2, te2; // second best score and ending position on the target
  18         int tb, qb; // target start and query start
  19 } kswr_t;
  20
  21 #ifdef __cplusplus
  22 extern "C" {
  23 #endif
  24
  25         /**
  26          * Aligning two sequences
  27          *
  28          * @param qlen    length of the query sequence (typically <tlen)
  29          * @param query   query sequence with 0 <= query[i] < m
  30          * @param tlen    length of the target sequence
  31          * @param target  target sequence
  32          * @param m       number of residue types
  33          * @param mat     m*m scoring matrix in one-dimention array
  34          * @param gapo    gap open penalty; a gap of length l cost "-(gapo+l*gape)"
  35          * @param gape    gap extension penalty
  36          * @param xtra    extra information (see below)
  37          * @param qry     query profile (see below)
  38          *
  39          * @return        alignment information in a struct; unset values to -1
  40          *
  41          * When xtra==0, ksw_align() uses a signed two-byte integer to store a
  42          * score and only finds the best score and the end positions. The 2nd best
  43          * score or the start positions are not attempted. The default behavior can
  44          * be tuned by setting KSW_X* flags:
  45          *
  46          *   KSW_XBYTE:  use an unsigned byte to store a score. If overflow occurs,
  47          *               kswr_t::score will be set to 255
  48          *
  49          *   KSW_XSUBO:  track the 2nd best score and the ending position on the
  50          *               target if the 2nd best is higher than (xtra&0xffff)
  51          *
  52          *   KSW_XSTOP:  stop if the maximum score is above (xtra&0xffff)
  53          *
  54          *   KSW_XSTART: find the start positions
  55          *
  56          * When *qry==NULL, ksw_align() will compute and allocate the query profile
  57          * and when the function returns, *qry will point to the profile, which can
  58          * be deallocated simply by free(). If one query is aligned against multiple
  59          * target sequences, *qry should be set to NULL during the first call and
  60          * freed after the last call. Note that qry can equal 0. In this case, the
  61          * query profile will be deallocated in ksw_align().
  62          */
  63         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);
  64
  65         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);
  66         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);
  67
  68 #ifdef __cplusplus
  69 }
  70 #endif
  71
  72 #endif