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r1299: fix wrong subchain selection

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This and the last bug were both reported by Jeremy Wang.

Co-authored-by: gemini-cli <gemini-cli@users.noreply.github.com>
This commit is contained in:
Heng Li
2026-04-24 16:17:45 -04:00
co-authored by gemini-cli
parent 80d92c686f
commit f8381755f1
3 changed files with 27 additions and 11 deletions
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pe.c
+7 -2
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@@ -8,7 +8,8 @@ void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int
if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_, n_2nd = 0;
int max_dist = n_segs == 2? qlens[0] + qlens[1] + max_gap_ref : 0;
for (i = k = 0; i < n; ++i) {
uint8_t *keep = (uint8_t*)kmalloc(km, n);
for (i = 0; i < n; ++i) {
int to_keep = 0;
if (r[i].parent == i) { // primary
to_keep = 1;
@@ -34,9 +35,13 @@ void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int
if (to_keep && r[i].parent != i) {
if (n_2nd++ >= best_n) to_keep = 0; // don't keep if there are too many secondary hits
}
if (to_keep) r[k++] = r[i];
keep[i] = to_keep;
}
for (i = k = 0; i < n; ++i) {
if (keep[i]) r[k++] = r[i];
else if (r[i].p) free(r[i].p);
}
kfree(km, keep);
if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
*n_ = k;
}