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more accurate chain weight

This commit is contained in:
Heng Li 2013-02-08 15:34:25 -05:00
parent 220fc39e9d
commit 2848d3045a
1 changed files with 16 additions and 2 deletions
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18
bwamem.c
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@ -251,8 +251,22 @@ int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain_t *chains)
a = malloc(sizeof(flt_aux_t) * n_chn);
for (i = 0; i < n_chn; ++i) {
mem_chain_t *c = &chains[i];
int w = 0;
for (j = 0; j < c->n; ++j) w += c->seeds[j].len; // FIXME: take care of seed overlaps
int64_t end;
int w = 0, tmp;
for (j = 0, end = 0; j < c->n; ++j) {
const mem_seed_t *s = &c->seeds[j];
if (s->qbeg >= end) w += s->len;
else if (s->qbeg + s->len > end) w += s->qbeg + s->len - end;
end = end > s->qbeg + s->len? end : s->qbeg + s->len;
}
tmp = w;
for (j = 0, end = 0; j < c->n; ++j) {
const mem_seed_t *s = &c->seeds[j];
if (s->rbeg >= end) w += s->len;
else if (s->rbeg + s->len > end) w += s->rbeg + s->len - end;
end = end > s->qbeg + s->len? end : s->qbeg + s->len;
}
w = w < tmp? w : tmp;
a[i].beg = c->seeds[0].qbeg;
a[i].end = c->seeds[c->n-1].qbeg + c->seeds[c->n-1].len;
a[i].w = w; a[i].p = c; a[i].p2 = 0;