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no effective changes

This commit is contained in:
Heng Li 2013-02-07 16:42:01 -05:00
parent ff3fea115c
commit 6ba11ab68c
1 changed files with 4 additions and 3 deletions
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7
bwamem.c
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@ -375,7 +375,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
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 #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);
qw = malloc(l * 2); qw = malloc(l * 2);
@ -385,10 +385,11 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
for (j = 0; j < t->len; ++j) { for (j = 0; j < t->len; ++j) {
int x = t->rbeg + j - (s->rbeg + s->len), y = t->qbeg + j - (s->qbeg + s->len); int x = t->rbeg + j - (s->rbeg + s->len), y = t->qbeg + j - (s->qbeg + s->len);
if (x < 0) continue; // overlap with the first seed if (x < 0) continue; // overlap with the first seed
if (qw[x] == -1) qw[x] = x > y? x - y : y - x; if (qw[x] == -1) qw[x] = (x > y? x - y : y - x) + 1; // FIXME: in principle, we should not need +1
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);
@ -500,7 +501,7 @@ static mem_alnreg_v find_alnreg(const mem_opt_t *opt, const bwt_t *bwt, const bn
s->seq[i] = nst_nt4_table[(int)s->seq[i]]; s->seq[i] = nst_nt4_table[(int)s->seq[i]];
chn = mem_chain(opt, bwt, s->l_seq, (uint8_t*)s->seq); chn = mem_chain(opt, bwt, s->l_seq, (uint8_t*)s->seq);
chn.n = mem_chain_flt(opt, chn.n, chn.a); chn.n = mem_chain_flt(opt, chn.n, chn.a);
//mem_print_chain(bns, &chn); // mem_print_chain(bns, &chn);
regs.n = regs.m = chn.n; regs.n = regs.m = chn.n;
regs.a = malloc(regs.n * sizeof(mem_alnreg_t)); regs.a = malloc(regs.n * sizeof(mem_alnreg_t));
for (i = 0; i < chn.n; ++i) { for (i = 0; i < chn.n; ++i) {