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fixed a silly bug in ksw_extend() 

Query return value is assigned to the target variable and vice versa...
This commit is contained in:
Heng Li 2013-02-05 17:29:03 -05:00
parent 1e16f3e701
commit 14e6a7bdb9
2 changed files with 6 additions and 4 deletions
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6
bwamem.c
View File

@ -331,6 +331,8 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
} }
} }
} }
//printf("[Q] "); for (i = qe; i < l_query; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
//printf("[R] "); for (i = re; i < rmax[1] - rmax[0]; ++i) putchar("ACGTN"[(int)rseq[i]]); putchar('\n');
a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, a->score, qw, &qle, &tle); a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, a->score, qw, &qle, &tle);
a->qe = qe + qle; a->re = rmax[0] + re + tle; a->qe = qe + qle; a->re = rmax[0] + re + tle;
free(qw); free(qw);
@ -347,8 +349,8 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
w += abs((a->re - a->rb) - (a->qe - a->qb)); w += abs((a->re - a->rb) - (a->qe - a->qb));
nw_score = ksw_global(a->qe - a->qb, query + a->qb, a->re - a->rb, rseq + (a->rb - rmax[0]), 5, opt->mat, opt->q, opt->r, w, &a->n_cigar, &a->cigar); nw_score = ksw_global(a->qe - a->qb, query + a->qb, a->re - a->rb, rseq + (a->rb - rmax[0]), 5, opt->mat, opt->q, opt->r, w, &a->n_cigar, &a->cigar);
printf("[%d] ", c->n); for (i = a->qb; i < a->qe; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n'); //printf("[Q] "); for (i = a->qb; i < a->qe; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
printf("[%d] ", c->n); for (i = a->rb; i < a->re; ++i) putchar("ACGTN"[(int)rseq[i - rmax[0]]]); putchar('\n'); //printf("[R] "); for (i = a->rb; i < a->re; ++i) putchar("ACGTN"[(int)rseq[i - rmax[0]]]); putchar('\n');
printf("[%d] score=%d,%d\t[%d,%d) <=> [%lld,%lld)\tis_all=%d\t", c->n, a->score, nw_score, a->qb, a->qe, a->rb, a->re, a->is_all); printf("[%d] score=%d,%d\t[%d,%d) <=> [%lld,%lld)\tis_all=%d\t", c->n, a->score, nw_score, a->qb, a->qe, a->rb, a->re, a->is_all);
for (i = 0; i < a->n_cigar; ++i) printf("%d%c", a->cigar[i]>>4, "MIDS"[a->cigar[i]&0xf]); for (i = 0; i < a->n_cigar; ++i) printf("%d%c", a->cigar[i]>>4, "MIDS"[a->cigar[i]&0xf]);
putchar('\n'); putchar('\n');

4
ksw.c
View File

@ -392,8 +392,8 @@ int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
//beg = 0; end = qlen; // uncomment this line for debugging //beg = 0; end = qlen; // uncomment this line for debugging
} }
free(eh); free(qp); free(eh); free(qp);
if (_qle) *_qle = max_i + 1; if (_qle) *_qle = max_j + 1;
if (_tle) *_tle = max_j + 1; if (_tle) *_tle = max_i + 1;
return max; return max;
} }