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r371: extend overlapping seeds 

to avoid misalignment in tandem repeats
This commit is contained in:
Heng Li 2013-04-04 00:43:43 -04:00
parent 1e118e0823
commit d7ca0885eb
2 changed files with 15 additions and 2 deletions
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15
bwamem.c
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@ -537,7 +537,20 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
w = max_gap < opt->w? max_gap : opt->w;
if (qd - rd < w && rd - qd < w) break;
}
if (i < av->n) continue;
if (i < av->n) { // the seed is (almost) contained in an existing alignment
for (i = k + 1; i < c->n; ++i) { // check overlapping seeds in the same chain
const mem_seed_t *t;
if (srt[i] == 0) continue;
t = &c->seeds[(uint32_t)srt[i]];
if (t->len < s->len * .95) continue; // only check overlapping if t is long enough; TODO: more efficient by early stopping
if (s->qbeg <= t->qbeg && s->qbeg + s->len >= t->qbeg && t->qbeg - s->qbeg != t->rbeg - s->rbeg) break;
if (t->qbeg <= s->qbeg && t->qbeg + t->len >= s->qbeg && s->qbeg - t->qbeg != s->rbeg - t->rbeg) break;
}
if (i == c->n) { // no overlapping seeds; then skip extension
srt[k] = 0; // mark that seed extension has not been performed
continue;
}
}
a = kv_pushp(mem_alnreg_t, *av);
memset(a, 0, sizeof(mem_alnreg_t));

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3-r370-beta"
#define PACKAGE_VERSION "0.7.3-r371-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);