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r376: reduce wasteful seed extension 

mainly for contig alignment
This commit is contained in:
Heng Li 2013-04-10 12:18:56 -04:00
parent 47520134e7
commit 499cf4c00d
2 changed files with 3 additions and 3 deletions
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4
bwamem.c
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@ -543,8 +543,8 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
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 (s->qbeg <= t->qbeg && s->qbeg + s->len - t->qbeg >= s->len>>2 && t->qbeg - s->qbeg != t->rbeg - s->rbeg) break;
if (t->qbeg <= s->qbeg && t->qbeg + t->len - s->qbeg >= s->len>>2 && 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

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3-r375-beta"
#define PACKAGE_VERSION "0.7.3-r376-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);