diff --git a/bwamem.c b/bwamem.c
index ae70af7..33c911d 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -27,6 +27,8 @@ mem_opt_t *mem_opt_init()
 	o->min_seed_len = 17;
 	o->max_occ = 10;
 	o->max_chain_gap = 10000;
+	o->mask_level = 0.50;
+	o->chain_drop_ratio = 0.33;
 	mem_fill_scmat(o->a, o->b, o->mat);
 	return o;
 }
@@ -218,18 +220,18 @@ void mem_chain_flt(const mem_opt_t *opt, mem_chain_t *chn)
 	for (i = 0; i < chn->n; ++i) {
 		mem_chain1_t *c = &chn->chains[i];
 		int w = 0;
-		for (j = 0; j < c->n; ++j) w += c->len;
+		for (j = 0; j < c->n; ++j) w += c->seeds[j].len;
 		a[i].beg = c->seeds[0].qbeg;
 		a[i].end = c->seeds[c->n-1].qbeg + c->seeds[c->n-1].len;
 		a[i].w = w;
 		a[i].p = c;
-		a[i].w2 = 0; a[i].p2 = 0;
+		a[i].p2 = 0;
 	}
 	ks_introsort(mem_flt, chn->n, a);
 	for (i = 1, n = 1; i < chn->n; ++i) {
 		for (j = 0; j < n; ++j) {
 			int b_max = a[j].beg > a[i].beg? a[j].beg : a[i].beg;
-			int e_min = e[j].end < a[i].end? a[j].end : a[i].end;
+			int e_min = a[j].end < a[i].end? a[j].end : a[i].end;
 			if (e_min > b_max) { // have overlap
 				int min_l = a[i].end - a[i].beg < a[j].end - a[j].beg? a[i].end - a[i].beg : a[j].end - a[j].beg;
 				if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
@@ -241,7 +243,27 @@ void mem_chain_flt(const mem_opt_t *opt, mem_chain_t *chn)
 		}
 		if (j == n) a[n++] = a[i]; // if have no significant overlap with better chains, keep it.
 	}
+	for (i = 0; i < n; ++i) { // mark chains to be kept
+		mem_chain1_t *c = (mem_chain1_t*)a[i].p;
+		if (c->n > 0) c->n = -c->n;
+		c = (mem_chain1_t*)a[i].p2;
+		if (c && c->n > 0) c->n = -c->n;
+	}
 	free(a);
+	for (i = 0; i < chn->n; ++i) { // free discarded chains
+		mem_chain1_t *c = &chn->chains[i];
+		if (c->n >= 0) {
+			free(c->seeds);
+			c->n = c->m = 0;
+		} else c->n = -c->n;
+	}
+	for (i = n = 0; i < chn->n; ++i) { // squeeze out discarded chains
+		if (chn->chains[i].n > 0) {
+			if (n != i) chn->chains[n++] = chn->chains[i];
+			else ++n;
+		}
+	}
+	chn->n = n;
 }
 
 /****************************************
diff --git a/bwamem.h b/bwamem.h
index 0484edf..adf57dd 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -15,6 +15,7 @@ typedef struct {
 	int a, b, q, r, w;
 	int min_seed_len, max_occ, max_chain_gap;
 	int8_t mat[25]; // scoring matrix; mat[0] == 0 if unset
+	float mask_level, chain_drop_ratio;
 } mem_opt_t;
 
 typedef struct {
@@ -47,6 +48,7 @@ mem_opt_t *mem_opt_init(void);
 void mem_fill_scmat(int a, int b, int8_t mat[25]);
 
 mem_chain_t mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq);
+void mem_chain_flt(const mem_opt_t *opt, mem_chain_t *chn);
 void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c, mem_aln_t *a);
 
 #ifdef __cplusplus
diff --git a/fastmap.c b/fastmap.c
index 797a22f..f02224a 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -51,6 +51,7 @@ int main_mem(int argc, char *argv[])
 		for (i = 0; i < seq->seq.l; ++i)
 			seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
 		chain = mem_chain(opt, bwt, seq->seq.l, (uint8_t*)seq->seq.s);
+		mem_chain_flt(opt, &chain);
 		for (i = 0; i < chain.n; ++i) {
 			mem_chain1_t *p = &chain.chains[i];
 			mem_aln_t a;