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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
parent 80d92c686f
commit f8381755f1
3 changed files with 27 additions and 11 deletions
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27
hit.c
View File

@@ -256,19 +256,25 @@ void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int chec
{ {
if (pri_ratio > 0.0f && *n_ > 0) { if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_, n_2nd = 0; int i, k, n = *n_, n_2nd = 0;
for (i = k = 0; i < n; ++i) { uint8_t *keep = (uint8_t*)kmalloc(km, n);
for (i = 0; i < n; ++i) {
int p = r[i].parent; int p = r[i].parent;
keep[i] = 0;
if (p == i || r[i].inv) { // primary or inversion if (p == i || r[i].inv) { // primary or inversion
r[k++] = r[i]; keep[i] = 1;
} else if ((r[i].score >= r[p].score * pri_ratio || r[i].score + min_diff >= r[p].score) && n_2nd < best_n) { } else if ((r[i].score >= r[p].score * pri_ratio || r[i].score + min_diff >= r[p].score) && n_2nd < best_n) {
if (!(r[i].qs == r[p].qs && r[i].qe == r[p].qe && r[i].rid == r[p].rid && r[i].rs == r[p].rs && r[i].re == r[p].re)) // not identical hits if (!(r[i].qs == r[p].qs && r[i].qe == r[p].qe && r[i].rid == r[p].rid && r[i].rs == r[p].rs && r[i].re == r[p].re)) // not identical hits
r[k++] = r[i], ++n_2nd; keep[i] = 1, ++n_2nd;
else if (r[i].p) free(r[i].p);
} else if (check_strand && n_2nd < best_n && r[i].score > min_strand_sc && r[i].rev != r[p].rev) { } else if (check_strand && n_2nd < best_n && r[i].score > min_strand_sc && r[i].rev != r[p].rev) {
r[i].strand_retained = 1; r[i].strand_retained = 1;
r[k++] = r[i], ++n_2nd; keep[i] = 1, ++n_2nd;
} else if (r[i].p) free(r[i].p); }
} }
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() if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
*n_ = k; *n_ = k;
} }
@@ -277,13 +283,18 @@ void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int chec
int mm_filter_strand_retained(int n_regs, mm_reg1_t *r) int mm_filter_strand_retained(int n_regs, mm_reg1_t *r)
{ {
int i, k; int i, k;
for (i = k = 0; i < n_regs; ++i) { uint8_t *keep = (uint8_t*)malloc(n_regs);
for (i = 0; i < n_regs; ++i) {
int p = r[i].parent; int p = r[i].parent;
if (!r[i].strand_retained || r[i].div < r[p].div * 5.0f || r[i].div < 0.01f) { keep[i] = (!r[i].strand_retained || r[i].div < r[p].div * 5.0f || r[i].div < 0.01f);
}
for (i = k = 0; i < n_regs; ++i) {
if (keep[i]) {
if (k < i) r[k++] = r[i]; if (k < i) r[k++] = r[i];
else ++k; else ++k;
} }
} }
free(keep);
return k; return k;
} }

2
minimap.h
View File

@@ -5,7 +5,7 @@
#include <stdio.h> #include <stdio.h>
#include <sys/types.h> #include <sys/types.h>
#define MM_VERSION "2.30-r1298-dirty" #define MM_VERSION "2.30-r1299-dirty"
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit #define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name #define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name

9
pe.c
View File

@@ -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) { if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_, n_2nd = 0; int i, k, n = *n_, n_2nd = 0;
int max_dist = n_segs == 2? qlens[0] + qlens[1] + max_gap_ref : 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; int to_keep = 0;
if (r[i].parent == i) { // primary if (r[i].parent == i) { // primary
to_keep = 1; 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 (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 (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); 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() if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
*n_ = k; *n_ = k;
} }