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code backup

This commit is contained in:
Heng Li 2013-02-02 15:14:24 -05:00
parent 00e5302219
commit d25a87cc50
3 changed files with 6 additions and 4 deletions
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6
bwamem.c
View File

@ -176,10 +176,10 @@ mem_chain_t mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uin
return chain;
}
mem_aln_t mem_chain2aln(int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c)
mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c)
{
mem_aln_t a;
int i, j;
int i, j, max, max_i;
int64_t len;
for (i = 0; i < c->n; ++i) {
mem_seed_t *s = &c->seeds[i];
@ -188,5 +188,7 @@ mem_aln_t mem_chain2aln(int64_t l_pac, const uint8_t *pac, int l_query, const ui
for (j = 0; j < s->len; ++j) putchar("ACGTN"[query[j+s->qbeg]]); putchar('\n');
free(seq);
}
for (i = max = 0, max_i = -1; i < c->n; ++i) // find the longest seed
if (max < c->seeds[i].len) max = c->seeds[i].len, max_i = i;
return a;
}

2
bwamem.h
View File

@ -45,7 +45,7 @@ const bwtintv_v *smem_next(smem_i *itr, int split_len);
mem_opt_t *mem_opt_init(void);
mem_chain_t mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq);
mem_aln_t mem_chain2aln(int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c);
mem_aln_t mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c);
#ifdef __cplusplus
}

2
fastmap.c
View File

@ -52,7 +52,7 @@ int main_mem(int argc, char *argv[])
chain = mem_chain(opt, bwt, seq->seq.l, (uint8_t*)seq->seq.s);
for (i = 0; i < chain.n; ++i) {
mem_chain1_t *p = &chain.chains[i];
mem_chain2aln(bns->l_pac, pac, seq->seq.l, (uint8_t*)seq->seq.s, p);
mem_chain2aln(opt, bns->l_pac, pac, seq->seq.l, (uint8_t*)seq->seq.s, p);
printf("%d\t%d", i, p->n);
for (j = 0; j < p->n; ++j) {
bwtint_t pos;