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check if every seed is included; not used for now

This commit is contained in:
Heng Li 2013-02-04 15:09:47 -05:00
parent 5bfa45a69b
commit f27bd18f20
2 changed files with 8 additions and 2 deletions
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8
bwamem.c
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@ -240,7 +240,13 @@ mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac,
a.qe = qe + qle; a.re = rmax[0] + re + tle;
} else a.qe = l_query, a.re = s->rbeg + s->len;
printf("[%d] score=%d\t[%d,%d)\t[%lld,%lld)\n", c->n, a.score, a.qb, a.qe, a.rb, a.re);
a.is_all = 1;
if (c->n > 1) { // check if all the seeds have been included
s = &c->seeds[c->n - 1];
if (s->qbeg + s->len > a.qe) a.is_all = 0;
}
printf("[%d] score=%d\t[%d,%d) <=> [%lld,%lld)\tis_all=%d\n", c->n, a.score, a.qb, a.qe, a.rb, a.re, a.is_all);
free(rseq);
return a;

2
bwamem.h
View File

@ -30,7 +30,7 @@ typedef struct {
typedef struct {
int64_t pos, rb, re;
int n_cigar, len, score, qb, qe;
int n_cigar, len, score, qb, qe, is_all;
uint32_t *cigar;
} mem_aln_t;