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write the mem_aln_t struct

This commit is contained in:
Heng Li 2013-02-04 15:02:56 -05:00
parent 666638a953
commit 5bfa45a69b
2 changed files with 17 additions and 11 deletions
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24
bwamem.c
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@ -199,10 +199,12 @@ static inline int cal_max_gap(const mem_opt_t *opt, int qlen)
mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c)
{
mem_aln_t a;
int i, j, qbeg, qend, score;
int64_t k, rlen, rbeg, rend, rmax[2], tmp;
int i, j, qbeg, qend;
int64_t rlen, rbeg, rend, rmax[2], tmp;
mem_seed_t *s;
uint8_t *rseq = 0;
memset(&a, 0, sizeof(mem_aln_t));
// get the start and end of the seeded region
rbeg = c->seeds[0].rbeg; qbeg = c->seeds[0].qbeg;
s = &c->seeds[c->n-1];
@ -223,19 +225,23 @@ mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac,
tmp = rbeg - rmax[0];
rs = malloc(tmp);
for (i = 0; i < tmp; ++i) rs[i] = rseq[tmp - 1 - i];
score = ksw_extend(qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, opt->w, c->seeds[0].len * opt->a, 0, &qle, &tle);
a.score = ksw_extend(qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, opt->w, c->seeds[0].len * opt->a, 0, &qle, &tle);
a.qb = qbeg - qle; a.rb = rbeg - tle;
free(qs); free(rs);
} else score = c->seeds[0].len * opt->a;
} else a.score = c->seeds[0].len * opt->a, a.qb = 0, a.rb = rbeg;
if (c->seeds[0].qbeg + c->seeds[0].len != l_query) { // right extension of the first seed
s = &c->seeds[0];
if (s->qbeg + s->len != l_query) { // right extension of the first seed
int qle, tle, qe, re;
s = &c->seeds[0];
qe = s->qbeg + s->len; re = s->rbeg + s->len - rmax[0];
for (j = 0; j < l_query - qe; ++j) putchar("ACGTN"[(int)query[j+qe]]); putchar('\n');
for (j = 0; j < rmax[1] - rmax[0] - re; ++j) putchar("ACGTN"[(int)rseq[j+re]]); putchar('\n');
score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, opt->w, score, 0, &qle, &tle);
printf("[%d] score=%d\tqle=%d\trle=%d\n", c->n, score, 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, 0, &qle, &tle);
a.qe = qe + qle; a.re = rmax[0] + re + tle;
} else a.qe = l_query, a.re = s->rbeg + s->len;
printf("[%d] score=%d\t[%d,%d)\t[%lld,%lld)\n", c->n, a.score, a.qb, a.qe, a.rb, a.re);
free(rseq);
return a;
}

4
bwamem.h
View File

@ -29,8 +29,8 @@ typedef struct {
} mem_chain_t;
typedef struct {
int64_t pos;
int n_cigar, len, score;
int64_t pos, rb, re;
int n_cigar, len, score, qb, qe;
uint32_t *cigar;
} mem_aln_t;