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shm works on small files, but not large ones 

I don't know why. SHMMAX, SHMALL and SHMMNI are large enough.
This commit is contained in:
Heng Li 2014-10-15 15:44:06 -04:00
parent 6a0952948d
commit bfd5e1840f
3 changed files with 22 additions and 7 deletions
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21
bwa.c
View File

@ -227,7 +227,7 @@ bwt_t *bwa_idx_load_bwt(const char *hint)
return bwt;
}
bwaidx_t *bwa_idx_load(const char *hint, int which)
bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which)
{
bwaidx_t *idx;
char *prefix;
@ -256,6 +256,11 @@ bwaidx_t *bwa_idx_load(const char *hint, int which)
return idx;
}
bwaidx_t *bwa_idx_load(const char *hint, int which)
{
return bwa_idx_load_from_disk(hint, which);
}
void bwa_idx_destroy(bwaidx_t *idx)
{
if (idx == 0) return;
@ -263,7 +268,10 @@ void bwa_idx_destroy(bwaidx_t *idx)
if (idx->bwt) bwt_destroy(idx->bwt);
if (idx->bns) bns_destroy(idx->bns);
if (idx->pac) free(idx->pac);
} else if (!idx->is_shm) free(idx->mem);
} else {
free(idx->bwt); free(idx->bns->anns); free(idx->bns);
if (!idx->is_shm) free(idx->mem);
}
free(idx);
}
@ -273,19 +281,20 @@ int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx)
int i;
// generate idx->bwt
x = sizeof(bwt_t); idx->bwt = (bwt_t*)(mem + k); k += x;
x = sizeof(bwt_t); idx->bwt = malloc(x); memcpy(idx->bwt, mem + k, x); k += x;
x = idx->bwt->n_sa * sizeof(bwtint_t); idx->bwt->sa = (bwtint_t*)(mem + k); k += x;
x = idx->bwt->bwt_size * 4; idx->bwt->bwt = (uint32_t*)(mem + k); k += x;
// generate idx->bns and idx->pac
x = sizeof(bntseq_t); idx->bns = (bntseq_t*)(mem + k); k += x;
x = sizeof(bntseq_t); idx->bns = malloc(x); memcpy(idx->bns, mem + k, x); k += x;
x = idx->bns->n_holes * sizeof(bntamb1_t); idx->bns->ambs = (bntamb1_t*)(mem + k); k += x;
x = idx->bns->n_seqs * sizeof(bntann1_t); idx->bns->anns = (bntann1_t*)(mem + k); k += x;
x = idx->bns->n_seqs * sizeof(bntann1_t); idx->bns->anns = malloc(x); memcpy(idx->bns->anns, mem + k, x); k += x;
for (i = 0; i < idx->bns->n_seqs; ++i) {
idx->bns->anns[i].name = (char*)(mem + k); k += strlen(idx->bns->anns[i].name) + 1;
idx->bns->anns[i].anno = (char*)(mem + k); k += strlen(idx->bns->anns[i].anno) + 1;
}
idx->pac = (uint8_t*)(mem + k);
idx->pac = (uint8_t*)(mem + k); k += idx->bns->l_pac/4+1;
assert(k == l_mem);
idx->l_mem = k; idx->mem = mem;
return 0;

2
bwa.h
View File

@ -44,6 +44,8 @@ extern "C" {
char *bwa_idx_infer_prefix(const char *hint);
bwt_t *bwa_idx_load_bwt(const char *hint);
bwaidx_t *bwa_idx_load_from_shm(const char *hint);
bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which);
bwaidx_t *bwa_idx_load(const char *hint, int which);
void bwa_idx_destroy(bwaidx_t *idx);
int bwa_idx2mem(bwaidx_t *idx);

6
fastmap.c
View File

@ -230,7 +230,11 @@ int main_mem(int argc, char *argv[])
} else update_a(opt, &opt0);
bwa_fill_scmat(opt->a, opt->b, opt->mat);
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
idx = bwa_idx_load_from_shm(argv[optind]);
if (idx == 0) {
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
} else if (bwa_verbose >= 3)
fprintf(stderr, "[M::%s] load the bwa index from shared memory\n", __func__);
if (ignore_alt)
for (i = 0; i < idx->bns->n_seqs; ++i)
idx->bns->anns[i].is_alt = 0;