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fixed a couple of unimportant bugs in SMEM

This commit is contained in:
Heng Li 2013-01-31 11:53:07 -05:00
parent 6641788d38
commit 543c719a54
1 changed files with 4 additions and 5 deletions
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9
bwt.c
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@ -311,20 +311,19 @@ int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv,
swap = curr; curr = prev; prev = swap;
for (i = x - 1; i >= -1; --i) { // backward search for MEMs
if (i >= 0 && q[i] > 3) break; // always stop at an ambiguous base as the FM-index does not have any.
c = i < 0? 0 : q[i];
c = i < 0? -1 : q[i] < 4? q[i] : -1; // c==-1 if i<0 or q[i] is an ambiguous base
for (j = 0, curr->n = 0; j < prev->n; ++j) {
bwtintv_t *p = &prev->a[j];
bwt_extend(bwt, p, ok, 1);
if (ok[c].x[2] < min_intv || i == -1) { // keep the hit if reaching the beginning or not extended further
if (curr->n == 0) { // curr->n to make sure there is no longer matches
if (c < 0 || ok[c].x[2] < min_intv) { // keep the hit if reaching the beginning or an ambiguous base or the intv is small enough
if (curr->n == 0) { // test curr->n>0 to make sure there is no longer matches
if (mem->n == 0 || i + 1 < mem->a[mem->n-1].info>>32) { // skip contained matches
ik = *p; ik.info |= (uint64_t)(i + 1)<<32;
kv_push(bwtintv_t, *mem, ik);
}
} // otherwise the match is contained in another longer match
}
if (ok[c].x[2] && (curr->n == 0 || ok[c].x[2] != curr->a[curr->n-1].x[2])) {
if (c >= 0 && (ok[c].x[2] && (curr->n == 0 || ok[c].x[2] != curr->a[curr->n-1].x[2]))) {
ok[c].info = p->info;
kv_push(bwtintv_t, *curr, ok[c]);
}