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further preparation for pairing

This commit is contained in:
Heng Li 2011-11-05 14:31:30 -04:00
parent 06687a33b9
commit a29b179045
1 changed files with 27 additions and 1 deletions
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28
bwtsw2_aux.c
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@ -66,6 +66,25 @@ void bsw2_destroy(bwtsw2_t *b)
free(b);
}
bwtsw2_t *bsw2_dup(const bwtsw2_t *b)
{
bwtsw2_t *p;
int i;
p = calloc(1, sizeof(bwtsw2_t));
p->max = p->n = b->n;
kroundup32(p->max);
p->hits = calloc(p->max, sizeof(bsw2hit_t));
p->n_cigar = calloc(p->max, sizeof(int));
p->cigar = calloc(p->max, sizeof(void*));
memcpy(p->hits, b->hits, p->n * sizeof(bsw2hit_t));
for (i = 0; i < p->n; ++i) {
p->n_cigar[i] = b->n_cigar[i];
p->cigar[i] = malloc(p->n_cigar[i] * 4);
memcpy(p->cigar[i], b->cigar[i], p->n_cigar[i] * 4);
}
return p;
}
#define __gen_ap(par, opt) do { \
int i; \
for (i = 0; i < 25; ++i) (par).matrix[i] = -(opt)->b; \
@ -470,6 +489,8 @@ static void bsw2_aln_core(int tid, bsw2seq_t *_seq, const bsw2opt_t *_opt, const
int x;
bsw2opt_t opt = *_opt;
bsw2global_t *pool = bsw2_global_init();
bwtsw2_t **buf;
buf = calloc(_seq->n, sizeof(void*));
for (x = 0; x < _seq->n; ++x) {
bsw2seq1_t *p = _seq->seq + x;
uint8_t *seq[2], *rseq[2];
@ -533,11 +554,16 @@ static void bsw2_aln_core(int tid, bsw2seq_t *_seq, const bsw2opt_t *_opt, const
} else b[1] = 0;
// generate CIGAR and print SAM
gen_cigar(&opt, l, seq, pac, b[0]);
print_hits(bns, &opt, p, b[0]);
buf[x] = bsw2_dup(b[0]);
// free
free(seq[0]);
bsw2_destroy(b[0]);
}
for (x = 0; x < _seq->n; ++x) {
print_hits(bns, &opt, &_seq->seq[x], buf[x]);
bsw2_destroy(buf[x]);
}
free(buf);
bsw2_global_destroy(pool);
}