r1200: added --rmq-inner and --dbg-seed-freq

lchain.c

@@ -149,7 +149,7 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
 					  int is_cdna, int n_seg, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
 { // TODO: make sure this works when n has more than 32 bits
 	int32_t *f, *t, *v, n_u, n_v, mmax_f = 0, max_drop = bw;
-	int64_t *p, i, j, max_ii, st = 0, n_iter = 0;
+	int64_t *p, i, j, max_ii, st = 0;
 	uint64_t *u;
 
 	if (_u) *_u = 0, *n_u_ = 0;
@@ -174,7 +174,6 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
 		for (j = i - 1; j >= st; --j) {
 			int32_t sc;
 			sc = comput_sc(&a[i], &a[j], max_dist_x, max_dist_y, bw, chn_pen_gap, chn_pen_skip, is_cdna, n_seg);
-			++n_iter;
 			if (sc == INT32_MIN) continue;
 			sc += f[j];
 			if (sc > max_f) {
@@ -204,6 +203,7 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
 		if (max_ii < 0 || (a[i].x - a[max_ii].x <= (int64_t)max_dist_x && f[max_ii] < f[i]))
 			max_ii = i;
 		if (mmax_f < max_f) mmax_f = max_f;
+		//fprintf(stderr, "X1\t%ld\t%ld:%d\t%ld\t%ld:%d\t%ld\t%ld\t%ld\n", (long)i, (long)(a[i].x>>32), (int32_t)a[i].x, (long)max_j, max_j<0?-1L:(long)(a[max_j].x>>32), max_j<0?-1:(int32_t)a[max_j].x, (long)max_f, (long)v[i], (long)mmax_f);
 	}
 
 	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
@@ -325,12 +325,11 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
 				krmq_interval(lc_elem, root_inner, &s, &lo, &hi);
 				if (lo) {
 					const lc_elem_t *q;
-					int32_t width, n_rmq_iter = 0;
+					int32_t width;
 					krmq_itr_t(lc_elem) itr;
 					krmq_itr_find(lc_elem, root_inner, lo, &itr);
 					while ((q = krmq_at(&itr)) != 0) {
 						if (q->y < (int32_t)a[i].y - max_dist_inner) break;
-						++n_rmq_iter;
 						j = q->i;
 						sc = f[j] + comput_sc_simple(&a[i], &a[j], chn_pen_gap, chn_pen_skip, 0, &width);
 						if (width <= bw) {

main.c

@@ -78,6 +78,8 @@ static ko_longopt_t long_options[] = {
 	{ "no-hash-name",   ko_no_argument,       353 },
 	{ "secondary-seq",  ko_no_argument,       354 },
 	{ "ds",             ko_no_argument,       355 },
+	{ "rmq-inner",      ko_required_argument, 356 },
+	{ "dbg-seed-freq",  ko_no_argument,       501 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -245,6 +247,8 @@ int main(int argc, char *argv[])
 		else if (c == 353) opt.flag |= MM_F_NO_HASH_NAME; // --no-hash-name
 		else if (c == 354) opt.flag |= MM_F_SECONDARY_SEQ; // --secondary-seq
 		else if (c == 355) opt.flag |= MM_F_OUT_DS; // --ds
+		else if (c == 356) opt.rmq_inner_dist = mm_parse_num(o.arg); // --rmq-inner
+		else if (c == 501) mm_dbg_flag |= MM_DBG_SEED_FREQ; // --dbg-seed-freq
 		else if (c == 330) {
 			fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
 		} else if (c == 314) { // --frag

minimap.h

@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.27-r1193"
+#define MM_VERSION "2.27-r1200-dirty"
 
 #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

mmpriv.h

@@ -14,6 +14,7 @@
 #define MM_DBG_PRINT_SEED    0x4
 #define MM_DBG_PRINT_ALN_SEQ 0x8
 #define MM_DBG_PRINT_CHAIN   0x10
+#define MM_DBG_SEED_FREQ     0x20
 
 #define MM_SEED_LONG_JOIN  (1ULL<<40)
 #define MM_SEED_IGNORE     (1ULL<<41)

seed.c

@@ -112,7 +112,8 @@ mm_seed_t *mm_collect_matches(void *km, int *_n_m, int qlen, int max_occ, int ma
 	}
 	for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) {
 		mm_seed_t *q = &m[i];
-		//fprintf(stderr, "X\t%d\t%d\t%d\n", q->q_pos>>1, q->n, q->flt);
+		if (mm_dbg_flag & MM_DBG_SEED_FREQ)
+			fprintf(stderr, "SF\t%d\t%d\t%d\n", q->q_pos>>1, q->n, q->flt);
 		if (q->flt) {
 			int en = (q->q_pos >> 1) + 1, st = en - q->q_span;
 			if (st > rep_en) {