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revert to fixed band

This commit is contained in:
Heng Li 2017-06-14 14:22:23 -04:00
parent d3f17b1e05
commit 78fe89d1ab
2 changed files with 24 additions and 1 deletions
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19
ksw2.c
View File

@ -11,6 +11,20 @@
#define kfree(km, ptr) free((ptr)) #define kfree(km, ptr) free((ptr))
#endif #endif
void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
{
int i, j;
a = a < 0? -a : a;
b = b > 0? -b : b;
for (i = 0; i < m - 1; ++i) {
for (j = 0; j < m - 1; ++j)
mat[i * m + j] = i == j? a : b;
mat[i * m + m - 1] = 0;
}
for (j = 0; j < m; ++j)
mat[(m - 1) * m + j] = 0;
}
typedef struct { typedef struct {
int32_t h, e; int32_t h, e;
} eh_t; } eh_t;
@ -170,8 +184,13 @@ int ksw_global(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t
for (i = 0; i < tlen; ++i) { // target sequence is in the outer loop for (i = 0; i < tlen; ++i) { // target sequence is in the outer loop
int32_t f = NEG_INF, h1, st, en, max = NEG_INF; int32_t f = NEG_INF, h1, st, en, max = NEG_INF;
int8_t *q = &qp[target[i] * qlen]; int8_t *q = &qp[target[i] * qlen];
#if 0
st = max_j > w? max_j - w : 0; st = max_j > w? max_j - w : 0;
en = max_j + w + 1 < qlen? max_j + w + 1 : qlen; en = max_j + w + 1 < qlen? max_j + w + 1 : qlen;
#else
st = i > w? i - w : 0;
en = i + w + 1 < qlen? i + w + 1 : qlen;
#endif
h1 = st > 0? NEG_INF : -gapoe - gape * (i + 1); h1 = st > 0? NEG_INF : -gapoe - gape * (i + 1);
f = st > 0? NEG_INF : -gapoe - gapoe - gape * i; // similarly, -gapoe*2: one del followed by one ins f = st > 0? NEG_INF : -gapoe - gapoe - gape * i; // similarly, -gapoe*2: one del followed by one ins
off[i] = st; off[i] = st;

6
ksw2.h
View File

@ -1,6 +1,8 @@
#ifndef KSW2_H_ #ifndef KSW2_H_
#define KSW2_H_ #define KSW2_H_
#include <stdint.h>
#ifdef __cplusplus #ifdef __cplusplus
extern "C" { extern "C" {
#endif #endif
@ -23,7 +25,9 @@ extern "C" {
* *
* @return score of the alignment * @return score of the alignment
*/ */
int ksw_global(void *km, 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_global(void *km, 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);
void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b);
#ifdef __cplusplus #ifdef __cplusplus
} }