From e8823a37098dcc98c28db2108ae785aacdd5aaad Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 1 May 2021 15:22:51 -0400
Subject: [PATCH] r1027: renamed hifi to map-hifi; changed default

---
 main.c     | 2 +-
 minimap2.1 | 8 +++++++-
 options.c  | 5 +++--
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/main.c b/main.c
index 1dae0ac..160801f 100644
--- a/main.c
+++ b/main.c
@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.18-r1026-dirty"
+#define MM_VERSION "2.18-r1027-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
diff --git a/minimap2.1 b/minimap2.1
index f132780..018d958 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -523,7 +523,7 @@ Available
 .I STR
 are:
 .RS
-.TP 8
+.TP 9
 .B map-pb
 PacBio/Oxford Nanopore read to reference mapping
 .RB ( -Hk19 )
@@ -536,6 +536,12 @@ more sensitive results in comparison to normal minimizers. For Oxford Nanopore
 data, normal minimizers are better, though not much. The effectiveness of HPC
 is determined by the sequencing error mode.
 .TP
+.B map-hifi
+PacBio HiFi reads to reference mapping
+.RB ( -k19
+.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -e100 -g10k
+.BR --min-occ-floor=100 ).
+.TP
 .B asm5
 Long assembly to reference mapping
 .RB ( -k19
diff --git a/options.c b/options.c
index 45212dd..a597962 100644
--- a/options.c
+++ b/options.c
@@ -91,10 +91,11 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		io->flag |= MM_I_HPC, io->k = 19;
 	} else if (strcmp(preset, "map-ont") == 0) {
 		io->flag = 0, io->k = 15;
-	} else if (strcmp(preset, "hifi") == 0 || strcmp(preset, "ccs") == 0) {
+	} else if (strcmp(preset, "map-hifi") == 0 || strcmp(preset, "map-ccs") == 0) {
 		io->flag = 0, io->k = 19, io->w = 19;
 		mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1;
-		mo->occ_dist = 100;
+		mo->max_gap = 10000;
+		mo->occ_dist = 500;
 		mo->min_mid_occ = 100;
 		mo->min_dp_max = 200;
 	} else if (strcmp(preset, "asm5") == 0) {