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r378: bugfix - wrong CIGAR 

This is actually caused by a bug in SSE2-SW, where the query begin may be
smaller than the true one if there is an exact tandem repeat.
This commit is contained in:
Heng Li 2013-04-19 12:00:37 -04:00
parent 2087dc162f
commit be11e27e12
3 changed files with 7 additions and 5 deletions
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6
bwape.c
View File

@ -404,7 +404,7 @@ bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const u
bwa_cigar_t *cigar = 0; bwa_cigar_t *cigar = 0;
ubyte_t *ref_seq; ubyte_t *ref_seq;
bwtint_t k, x, y, l; bwtint_t k, x, y, l;
int xtra; int xtra, gscore;
int8_t mat[25]; int8_t mat[25];
bwa_fill_scmat(1, 3, mat); bwa_fill_scmat(1, 3, mat);
@ -422,12 +422,12 @@ bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const u
// do alignment // do alignment
xtra = KSW_XSUBO | KSW_XSTART | (len < 250? KSW_XBYTE : 0); xtra = KSW_XSUBO | KSW_XSTART | (len < 250? KSW_XBYTE : 0);
r = ksw_align(len, (uint8_t*)seq, l, ref_seq, 5, mat, 5, 1, xtra, 0); r = ksw_align(len, (uint8_t*)seq, l, ref_seq, 5, mat, 5, 1, xtra, 0);
ksw_global(r.qe - r.qb + 1, &seq[r.qb], r.te - r.tb + 1, &ref_seq[r.tb], 5, mat, 5, 1, 50, n_cigar, &cigar32); gscore = ksw_global(r.qe - r.qb + 1, &seq[r.qb], r.te - r.tb + 1, &ref_seq[r.tb], 5, mat, 5, 1, 50, n_cigar, &cigar32);
cigar = (bwa_cigar_t*)cigar32; cigar = (bwa_cigar_t*)cigar32;
for (k = 0; k < *n_cigar; ++k) for (k = 0; k < *n_cigar; ++k)
cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4)); cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));
if (r.score < SW_MIN_MATCH_LEN || r.score2 == r.score) { // poor hit or tandem hits if (r.score < SW_MIN_MATCH_LEN || r.score2 == r.score || gscore != r.score) { // poor hit or tandem hits or weird alignment
free(cigar); free(ref_seq); *n_cigar = 0; free(cigar); free(ref_seq); *n_cigar = 0;
return 0; return 0;
} }

4
ksw.c
View File

@ -201,10 +201,11 @@ end_loop16:
r.score = gmax + q->shift < 255? gmax : 255; r.score = gmax + q->shift < 255? gmax : 255;
r.te = te; r.te = te;
if (r.score != 255) { // get a->qe, the end of query match; find the 2nd best score if (r.score != 255) { // get a->qe, the end of query match; find the 2nd best score
int max = -1, low, high, qlen = slen * 16; int max = -1, tmp, low, high, qlen = slen * 16;
uint8_t *t = (uint8_t*)Hmax; uint8_t *t = (uint8_t*)Hmax;
for (i = 0; i < qlen; ++i, ++t) for (i = 0; i < qlen; ++i, ++t)
if ((int)*t > max) max = *t, r.qe = i / 16 + i % 16 * slen; if ((int)*t > max) max = *t, r.qe = i / 16 + i % 16 * slen;
else ((int)*t == max && (tmp = i / 16 + i % 16 * slen) < r.qe) r.qe = tmp;
//printf("%d,%d\n", max, gmax); //printf("%d,%d\n", max, gmax);
if (b) { if (b) {
i = (r.score + q->max - 1) / q->max; i = (r.score + q->max - 1) / q->max;
@ -306,6 +307,7 @@ end_loop8:
uint16_t *t = (uint16_t*)Hmax; uint16_t *t = (uint16_t*)Hmax;
for (i = 0, r.qe = -1; i < qlen; ++i, ++t) for (i = 0, r.qe = -1; i < qlen; ++i, ++t)
if ((int)*t > max) max = *t, r.qe = i / 8 + i % 8 * slen; if ((int)*t > max) max = *t, r.qe = i / 8 + i % 8 * slen;
else ((int)*t == max && (tmp = i / 8 + i % 8 * slen) < r.qe) r.qe = tmp;
if (b) { if (b) {
i = (r.score + q->max - 1) / q->max; i = (r.score + q->max - 1) / q->max;
low = te - i; high = te + i; low = te - i; high = te + i;

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3-r377-beta" #define PACKAGE_VERSION "0.7.3-r378-beta"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);