From 89d4d219cd93c778c9053c322babfe1f6e6c1329 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 20 Mar 2024 15:29:54 -0400
Subject: [PATCH] r1206: enabled RMQ for lr:hqae

Also fixed a bug in determining inner_dist for RMQ. It should have no effect on
previous presets.
---
 align.c   | 4 ++--
 lchain.c  | 5 +++--
 minimap.h | 2 +-
 options.c | 1 +
 4 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/align.c b/align.c
index a1d90ea6..9586dd80 100644
--- a/align.c
+++ b/align.c
@@ -933,14 +933,14 @@ double mm_event_identity(const mm_reg1_t *r)
 static int32_t mm_recal_max_dp(const mm_reg1_t *r, double b2, int32_t match_sc)
 {
 	uint32_t i;
-	int32_t n_gap = 0, n_gapo = 0, n_mis;
+	int32_t n_gap = 0, n_mis;
 	double gap_cost = 0.0;
 	if (r->p == 0) return -1;
 	for (i = 0; i < r->p->n_cigar; ++i) {
 		int32_t op = r->p->cigar[i] & 0xf, len = r->p->cigar[i] >> 4;
 		if (op == MM_CIGAR_INS || op == MM_CIGAR_DEL) {
 			gap_cost += b2 + (double)mg_log2(1.0 + len);
-			++n_gapo, n_gap += len;
+			n_gap += len;
 		}
 	}
 	n_mis = r->blen + r->p->n_ambi - r->mlen - n_gap;
diff --git a/lchain.c b/lchain.c
index 9c76517b..d20aa3ab 100644
--- a/lchain.c
+++ b/lchain.c
@@ -203,7 +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);
+		//fprintf(stderr, "X1\t%ld\t%ld:%d\t%ld\t%ld:%d\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]);
 	}
 
 	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
@@ -263,7 +263,8 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
 		return 0;
 	}
 	if (max_dist < bw) max_dist = bw;
-	if (max_dist_inner <= 0 || max_dist_inner >= max_dist) max_dist_inner = 0;
+	if (max_dist_inner < 0) max_dist_inner = 0;
+	if (max_dist_inner > max_dist) max_dist_inner = max_dist;
 	p = Kmalloc(km, int64_t, n);
 	f = Kmalloc(km, int32_t, n);
 	t = Kcalloc(km, int32_t, n);
diff --git a/minimap.h b/minimap.h
index 54f85965..8930cd5d 100644
--- a/minimap.h
+++ b/minimap.h
@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.27-r1205-dirty"
+#define MM_VERSION "2.27-r1206-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
diff --git a/options.c b/options.c
index cd2990d1..5dd6af95 100644
--- a/options.c
+++ b/options.c
@@ -116,6 +116,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		}
 	} else if (strcmp(preset, "lr:hqae") == 0) { // high-quality assembly evaluation
 		io->flag = 0, io->k = 25, io->w = 51;
+		mo->flag |= MM_F_RMQ;
 		mo->min_mid_occ = 50, mo->max_mid_occ = 500;
 		mo->rmq_inner_dist = 5000;
 		mo->occ_dist = 200;