From d3a89d34d49a54edf7d21f13f516171494f13516 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 23 Dec 2021 20:43:54 -0500
Subject: [PATCH] r1118: use -r1k,100k for asm* modes

---
 main.c     | 2 +-
 minimap2.1 | 6 +++---
 options.c  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/main.c b/main.c
index 900bd08..1455ca0 100644
--- a/main.c
+++ b/main.c
@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.23-r1117-dirty"
+#define MM_VERSION "2.23-r1118-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/minimap2.1 b/minimap2.1
index 7d0c2c5..666de78 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -565,7 +565,7 @@ Align older PacBio continuous long (CLR) reads to a reference genome
 .B asm5
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
+.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
 .BR -N50 ).
 Typically, the alignment will not extend to regions with 5% or higher sequence
 divergence. Only use this preset if the average divergence is far below 5%.
@@ -573,14 +573,14 @@ divergence. Only use this preset if the average divergence is far below 5%.
 .B asm10
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
+.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
 .BR -N50 ).
 Up to 10% sequence divergence.
 .TP
 .B asm20
 Long assembly to reference mapping
 .RB ( -k19
-.B -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
+.B -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
 .BR -N50 ).
 Up to 20% sequence divergence.
 .TP
diff --git a/options.c b/options.c
index 285c57b..18aafdc 100644
--- a/options.c
+++ b/options.c
@@ -113,7 +113,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mo->min_dp_max = 200;
 	} else if (strncmp(preset, "asm", 3) == 0) {
 		io->flag = 0, io->k = 19, io->w = 19;
-		mo->bw = mo->bw_long = 100000;
+		mo->bw = 1000, mo->bw_long = 100000;
 		mo->max_gap = 10000;
 		mo->flag |= MM_F_RMQ;
 		mo->min_mid_occ = 50, mo->max_mid_occ = 500;