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better treatment for micro-repeat

This commit is contained in:
Heng Li 2013-02-07 21:20:36 -05:00
parent 45b0d3423a
commit d890c7997c
1 changed files with 52 additions and 48 deletions
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52
bwamem.c
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@ -344,12 +344,13 @@ static inline int cal_max_gap(const mem_opt_t *opt, int qlen)
void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_t *a) void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_t *a)
{ // FIXME: in general, we SHOULD check funny seed patterns such as contained seeds. When that happens, we should use a SW or extend more seeds { // FIXME: in general, we SHOULD check funny seed patterns such as contained seeds. When that happens, we should use a SW or extend more seeds
int i, qbeg, max = 0, max_i = -1; int i, k;
int64_t rlen, rbeg, rmax[2], tmp; int64_t rlen, rmax[2], tmp, max = 0, max_i = 0;
const mem_seed_t *s; const mem_seed_t *s;
uint8_t *rseq = 0; uint8_t *rseq = 0;
mem_alnreg_t best;
memset(a, 0, sizeof(mem_alnreg_t)); memset(&best, 0, sizeof(mem_alnreg_t));
// get the max possible span // get the max possible span
rmax[0] = l_pac<<1; rmax[1] = 0; rmax[0] = l_pac<<1; rmax[1] = 0;
for (i = 0; i < c->n; ++i) { for (i = 0; i < c->n; ++i) {
@ -359,31 +360,32 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
e = t->rbeg + t->len + ((l_query - t->qbeg - t->len) + cal_max_gap(opt, l_query - t->qbeg - t->len)); e = t->rbeg + t->len + ((l_query - t->qbeg - t->len) + cal_max_gap(opt, l_query - t->qbeg - t->len));
rmax[0] = rmax[0] < b? rmax[0] : b; rmax[0] = rmax[0] < b? rmax[0] : b;
rmax[1] = rmax[1] > e? rmax[1] : e; rmax[1] = rmax[1] > e? rmax[1] : e;
if (max < t->len) max = t->len, max_i = i; if (t->len > max) max = t->len, max_i = i;
} }
// get the start and end of the seeded region
rbeg = c->seeds[max_i].rbeg; qbeg = c->seeds[max_i].qbeg;
// retrieve the reference sequence // retrieve the reference sequence
rseq = bns_get_seq(l_pac, pac, rmax[0], rmax[1], &rlen); rseq = bns_get_seq(l_pac, pac, rmax[0], rmax[1], &rlen);
if (qbeg) { // left extension of the first seed for (k = 0; k < c->n;) {
s = &c->seeds[k];
memset(a, 0, sizeof(mem_alnreg_t));
if (s->qbeg) { // left extension
uint8_t *rs, *qs; uint8_t *rs, *qs;
int qle, tle; int qle, tle;
qs = malloc(qbeg); qs = malloc(s->qbeg);
for (i = 0; i < qbeg; ++i) qs[i] = query[qbeg - 1 - i]; for (i = 0; i < s->qbeg; ++i) qs[i] = query[s->qbeg - 1 - i];
tmp = rbeg - rmax[0]; tmp = s->rbeg - rmax[0];
rs = malloc(tmp); rs = malloc(tmp);
for (i = 0; i < tmp; ++i) rs[i] = rseq[tmp - 1 - i]; for (i = 0; i < tmp; ++i) rs[i] = rseq[tmp - 1 - i];
a->score = ksw_extend(qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, opt->w, c->seeds[max_i].len * opt->a, 0, &qle, &tle); a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, opt->w, s->len * opt->a, 0, &qle, &tle);
a->qb = qbeg - qle; a->rb = rbeg - tle; a->qb = s->qbeg - qle; a->rb = s->rbeg - tle;
free(qs); free(rs); free(qs); free(rs);
} else a->score = c->seeds[max_i].len * opt->a, a->qb = 0, a->rb = rbeg; } else a->score = s->len * opt->a, a->qb = 0, a->rb = s->rbeg;
s = &c->seeds[max_i];
if (s->qbeg + s->len != l_query) { // right extension of the first seed if (s->qbeg + s->len != l_query) { // right extension of the first seed
int qle, tle, qe, re; int qle, tle, qe, re;
int16_t *qw = 0; int16_t *qw = 0;
qe = s->qbeg + s->len; re = s->rbeg + s->len - rmax[0]; qe = s->qbeg + s->len;
re = s->rbeg + s->len - rmax[0];
#if 0 // FIXME: I am not sure if the following block works. Comment it out if SW extension gives unexpected result. #if 0 // FIXME: I am not sure if the following block works. Comment it out if SW extension gives unexpected result.
if (c->n > 1) { // generate $qw if (c->n > 1) { // generate $qw
int j, l = rmax[1] - (s->rbeg + s->len); int j, l = rmax[1] - (s->rbeg + s->len);
@ -398,22 +400,24 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
else if (qw[x] >= 0) qw[x] = -2; // in a seed overlap, do not set any constraint else if (qw[x] >= 0) qw[x] = -2; // in a seed overlap, do not set any constraint
} }
} }
// for (i = 0; i < l; ++i) printf("%d:%d\t", i, qw[i]); putchar('\n');
} }
#endif #endif
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);
} else a->qe = l_query, a->re = s->rbeg + s->len; } else a->qe = l_query, a->re = s->rbeg + s->len;
/* if (mem_debug >= 2) printf("[%d] score=%d\t[%d,%d) <=> [%ld,%ld)\n", k, a->score, a->qb, a->qe, (long)a->rb, (long)a->re);
a->is_all = 1; // check how many seeds have been covered
if (c->n > 1) { // check if all the seeds have been included for (i = k + 1; i < c->n; ++i) {
s = &c->seeds[c->n - 1]; const mem_seed_t *t = &c->seeds[i];
if (s->qbeg + s->len > a->qe) a->is_all = 0; if (t->rbeg + t->len > a->re || t->qbeg + t->len > a->qe)
break;
} }
*/ if (i >= c->n) break; // all seeds are included; no need to proceed
if (mem_debug >= 2) if (a->score > best.score) best = *a;
printf("[%d] score=%d\t[%d,%d) <=> [%lld,%lld)\n", c->n, a->score, a->qb, a->qe, a->rb, a->re); k = i;
}
if (a->score < best.score) *a = best;
free(rseq); free(rseq);
} }