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fixed a deadlock; SMEM iterator

This commit is contained in:
Heng Li 2011-11-24 19:15:14 -05:00
parent b5170e0efa
commit 150bfbdef4
3 changed files with 83 additions and 51 deletions
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26
bwt.c
View File

@ -292,13 +292,17 @@ int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, bwtintv_v *mem
ik.info = x + 1;
for (i = x + 1, curr->n = 0; i < len; ++i) { // forward search
if (q[i] > 3) break;
if (q[i] < 4) {
c = 3 - q[i];
bwt_extend(bwt, &ik, ok, 0);
if (ok[c].x[2] != ik.x[2]) // change of the interval size
kv_push(bwtintv_t, *curr, ik);
if (ok[c].x[2] == 0) break; // cannot be extended
ik = ok[c]; ik.info = i + 1;
} else { // an ambiguous base
kv_push(bwtintv_t, *curr, ik);
break; // cannot be extended; in this case, i<len always stands
}
}
if (i == len) kv_push(bwtintv_t, *curr, ik); // push the last interval if we reach the end
bwt_reverse_intvs(curr); // s.t. smaller intervals visited first
@ -333,23 +337,3 @@ int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, bwtintv_v *mem
if (tmpvec[1] == 0) free(a[1].a);
return ret;
}
int bwt_smem(const bwt_t *bwt, int len, const uint8_t *q, bwtintv_v *mem, bwtintv_v *tmpvec[3])
{
int x = 0, i;
bwtintv_v a[3], *tvec[2], *mem1;
kv_init(a[0]); kv_init(a[1]); kv_init(a[2]); // no memory allocation here
tvec[0] = tmpvec[0]? tmpvec[0] : &a[0];
tvec[1] = tmpvec[1]? tmpvec[1] : &a[1];
mem1 = tmpvec[2]? tmpvec[2] : &a[2];
mem->n = 0;
do {
x = bwt_smem1(bwt, len, q, x, mem1, tvec);
for (i = 0; i < mem1->n; ++i)
kv_push(bwtintv_t, *mem, mem1->a[i]);
} while (x < len);
if (tmpvec[0] == 0) free(a[0].a);
if (tmpvec[1] == 0) free(a[1].a);
if (tmpvec[2] == 0) free(a[2].a);
return mem->n;
}

10
bwt.h
View File

@ -112,8 +112,16 @@ extern "C" {
int bwt_match_exact(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *sa_begin, bwtint_t *sa_end);
int bwt_match_exact_alt(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *k0, bwtint_t *l0);
/**
* Extend bi-SA-interval _ik_
*/
void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_back);
int bwt_smem(const bwt_t *bwt, int len, const uint8_t *q, bwtintv_v *mem, bwtintv_v *tmpvec[3]);
/**
* Given a query _q_, collect potential SMEMs covering position _x_ and store them in _mem_.
* Return the end of the longest exact match starting from _x_.
*/
int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
#ifdef __cplusplus
}

64
fastmap.c
View File

@ -10,6 +10,49 @@ KSEQ_INIT(gzFile, gzread)
extern unsigned char nst_nt4_table[256];
typedef struct {
const bwt_t *bwt;
const uint8_t *query;
int start, len;
bwtintv_v *tmpvec[2], *matches;
} smem_i;
smem_i *smem_iter_init(const bwt_t *bwt)
{
smem_i *iter;
iter = calloc(1, sizeof(smem_i));
iter->bwt = bwt;
iter->tmpvec[0] = calloc(1, sizeof(bwtintv_v));
iter->tmpvec[1] = calloc(1, sizeof(bwtintv_v));
iter->matches = calloc(1, sizeof(bwtintv_v));
return iter;
}
void smem_iter_destroy(smem_i *iter)
{
free(iter->tmpvec[0]->a);
free(iter->tmpvec[1]->a);
free(iter->matches->a);
free(iter);
}
void smem_set_query(smem_i *iter, int len, const uint8_t *query)
{
iter->query = query;
iter->start = 0;
iter->len = len;
}
int smem_next(smem_i *iter)
{
iter->tmpvec[0]->n = iter->tmpvec[1]->n = iter->matches->n = 0;
if (iter->start >= iter->len || iter->start < 0) return -1;
while (iter->start < iter->len && iter->query[iter->start] > 3) ++iter->start; // skip ambiguous bases
if (iter->start == iter->len) return -1;
iter->start = bwt_smem1(iter->bwt, iter->len, iter->query, iter->start, iter->matches, iter->tmpvec);
return iter->start;
}
int main_fastmap(int argc, char *argv[])
{
int c, i, min_iwidth = 20, min_len = 17;
@ -18,7 +61,7 @@ int main_fastmap(int argc, char *argv[])
gzFile fp;
bwt_t *bwt;
bntseq_t *bns;
bwtintv_v a[3], mem, *tvec[3];
smem_i *iter;
while ((c = getopt(argc, argv, "w:l:")) >= 0) {
switch (c) {
@ -42,18 +85,15 @@ int main_fastmap(int argc, char *argv[])
free(tmp);
bns = bns_restore(argv[optind]);
}
for (i = 0; i < 3; ++i) { // initiate the temporary array
kv_init(a[i]);
tvec[i] = &a[i];
}
kv_init(mem);
iter = smem_iter_init(bwt);
while (kseq_read(seq) >= 0) {
for (i = 0; i < seq->seq.l; ++i)
seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
bwt_smem(bwt, seq->seq.l, (uint8_t*)seq->seq.s, &mem, tvec);
printf("SQ\t%s\t%ld\n", seq->name.s, seq->seq.l);
for (i = 0; i < mem.n; ++i) {
bwtintv_t *p = &mem.a[i];
smem_set_query(iter, seq->seq.l, (uint8_t*)seq->seq.s);
while (smem_next(iter) > 0) {
for (i = 0; i < iter->matches->n; ++i) {
bwtintv_t *p = &iter->matches->a[i];
if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
if (p->x[2] <= min_iwidth) {
@ -66,14 +106,14 @@ int main_fastmap(int argc, char *argv[])
bns_cnt_ambi(bns, pos, len, &ref_id);
printf("\t%s:%c%ld", bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - bns->anns[ref_id].offset) + 1);
}
}
} else fputs("\t*", stdout);
putchar('\n');
}
}
puts("//");
}
free(mem.a);
for (i = 0; i < 3; ++i) free(a[i].a);
smem_iter_destroy(iter);
bns_destroy(bns);
bwt_destroy(bwt);
kseq_destroy(seq);