From cf55c8405629922267f8d1957a464f7427bd419e Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 4 Oct 2017 12:08:44 -0400
Subject: [PATCH] r460: added option --no-long-join

---
 main.c    | 4 +++-
 map.c     | 2 +-
 minimap.h | 1 +
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/main.c b/main.c
index 88194ff..cf43b51 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r459-dirty"
+#define MM_VERSION "2.2-r460-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -38,6 +38,7 @@ static struct option long_options[] = {
 	{ "no-sam-sq",      no_argument,       0, 0 },
 	{ "sr",             no_argument,       0, 0 },
 	{ "multi-seg",      optional_argument, 0, 0 },
+	{ "no-long-join",   no_argument,       0, 0 },
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -116,6 +117,7 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
 		else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_SAM_SQ; // --no-sam-sq
 		else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
+		else if (c == 0 && long_idx ==15) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
 		else if (c == 0 && long_idx ==14) { // --multi-seg
 			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
 				opt.flag |= MM_F_MULTI_SEG;
diff --git a/map.c b/map.c
index 6c747bd..5492e8c 100644
--- a/map.c
+++ b/map.c
@@ -242,7 +242,7 @@ static void chain_post(const mm_mapopt_t *opt, const mm_idx_t *mi, void *km, int
 		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
 		if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
 		else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, opt->max_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
-		if (!(opt->flag & MM_F_SPLICE) && !(opt->flag & MM_F_SR))
+		if (!(opt->flag & MM_F_SPLICE) && !(opt->flag & MM_F_SR) && !(opt->flag & MM_F_NO_LJOIN))
 			mm_join_long(km, opt, qlen, n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
 	}
 }
diff --git a/minimap.h b/minimap.h
index 55ab281..349c8e9 100644
--- a/minimap.h
+++ b/minimap.h
@@ -15,6 +15,7 @@
 #define MM_F_SPLICE      0x080 // splice mode
 #define MM_F_SPLICE_FOR  0x100 // match GT-AG
 #define MM_F_SPLICE_REV  0x200 // match CT-AC, the reverse complement of GT-AG
+#define MM_F_NO_LJOIN    0x400
 #define MM_F_NO_SAM_SQ   0x800
 #define MM_F_SR          0x1000
 #define MM_F_MULTI_SEG   0x2000