diff --git a/hit.c b/hit.c
index 9dfa7a4..ae74941 100644
--- a/hit.c
+++ b/hit.c
@@ -304,7 +304,7 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
 	for (i = n_aux - 1; i >= 1; --i) {
 		mm_reg1_t *r0 = &regs[(int32_t)aux[i-1]], *r1 = &regs[(int32_t)aux[i]];
 		mm128_t *a0e, *a1s;
-		int max_gap, min_gap, sc_thres;
+		int max_gap, min_gap, sc_thres, min_flank_len;
 
 		// test
 		if (r0->as + r0->cnt != r1->as) continue; // not adjacent in a[]
@@ -318,8 +318,9 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_r
 		if (max_gap > opt->max_join_long || min_gap > opt->max_join_short) continue;
 		sc_thres = (int)((float)opt->min_join_flank_sc / opt->max_join_long * max_gap + .499);
 		if (r0->score < sc_thres || r1->score < sc_thres) continue; // require good flanking chains
-		if (r0->re - r0->rs < max_gap>>1 || r0->qe - r0->qs < max_gap>>1) continue; // require enough flanking length
-		if (r1->re - r1->rs < max_gap>>1 || r1->qe - r1->qs < max_gap>>1) continue;
+		min_flank_len = (int)(max_gap * opt->min_join_flank_ratio);
+		if (r0->re - r0->rs < min_flank_len || r0->qe - r0->qs < min_flank_len) continue; // require enough flanking length
+		if (r1->re - r1->rs < min_flank_len || r1->qe - r1->qs < min_flank_len) continue;
 
 		// all conditions satisfied; join
 		a[r1->as].y |= MM_SEED_LONG_JOIN;
diff --git a/main.c b/main.c
index 2192a89..755fffe 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "getopt.h"
 #endif
 
-#define MM_VERSION "2.10-r761"
+#define MM_VERSION "2.10-r763-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -57,6 +57,7 @@ static struct option long_options[] = {
 	{ "max-clip-ratio", required_argument, 0, 0 },   // 27
 	{ "min-occ-floor",  required_argument, 0, 0 },   // 28
 	{ "MD",             no_argument,       0, 0 },   // 29
+	{ "lj-min-ratio",   required_argument, 0, 0 },   // 30
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -173,6 +174,7 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==27) opt.max_clip_ratio = atof(optarg); // --max-clip-ratio
 		else if (c == 0 && long_idx ==28) opt.min_mid_occ = atoi(optarg); // --min-occ-floor
 		else if (c == 0 && long_idx ==29) opt.flag |= MM_F_OUT_MD; // --MD
+		else if (c == 0 && long_idx ==30) opt.min_join_flank_ratio = atof(optarg); // --lj-min-ratio
 		else if (c == 0 && long_idx == 14) { // --frag
 			yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
 		} else if (c == 0 && long_idx == 15) { // --secondary
diff --git a/minimap.h b/minimap.h
index 7d416a1..d87c891 100644
--- a/minimap.h
+++ b/minimap.h
@@ -115,6 +115,7 @@ typedef struct {
 
 	int max_join_long, max_join_short;
 	int min_join_flank_sc;
+	float min_join_flank_ratio;
 
 	int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
 	int noncan;      // cost of non-canonical splicing sites
diff --git a/options.c b/options.c
index 04807c5..5c19978 100644
--- a/options.c
+++ b/options.c
@@ -31,6 +31,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 	opt->max_join_long = 20000;
 	opt->max_join_short = 2000;
 	opt->min_join_flank_sc = 1000;
+	opt->min_join_flank_ratio = 0.5f;
 
 	opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1;
 	opt->zdrop = 400, opt->zdrop_inv = 200;
diff --git a/python/cmappy.pxd b/python/cmappy.pxd
index adef28f..231f68f 100644
--- a/python/cmappy.pxd
+++ b/python/cmappy.pxd
@@ -24,6 +24,7 @@ cdef extern from "minimap.h":
 		int best_n
 		int max_join_long, max_join_short
 		int min_join_flank_sc
+		float min_join_flank_ratio;
 		int a, b, q, e, q2, e2
 		int noncan
 		int zdrop, zdrop_inv