added two more filters

main.c

@@ -69,6 +69,8 @@ static ko_longopt_t long_options[] = {
 	{ "sam-hit-only",   ko_no_argument,       342 },
 	{ "idx-min-occ",    ko_required_argument, 343 },
 	{ "idx-max-occ",    ko_required_argument, 344 },
+	{ "flt-max-dv",     ko_required_argument, 345 },
+	{ "flt-min-blen",   ko_required_argument, 346 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -214,6 +216,8 @@ int main(int argc, char *argv[])
 		else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
 		else if (c == 343) ipt.min_occ = mm_parse_num(o.arg); // --idx-min-occ
 		else if (c == 344) ipt.max_occ = mm_parse_num(o.arg); // --idx-max-occ
+		else if (c == 345) opt.flt_max_dv = atof(o.arg); // --flt-max-dv
+		else if (c == 346) opt.flt_min_blen = mm_parse_num(o.arg); // --flt-min-blen
 		else if (c == 314) { // --frag
 			yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
 		} else if (c == 315) { // --secondary

map.c

@@ -351,6 +351,15 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 
 	chain_post(opt, max_chain_gap_ref, mi, b->km, qlen_sum, n_segs, qlens, &n_regs0, regs0, a);
 	if (!is_sr) mm_est_err(mi, qlen_sum, n_regs0, regs0, a, n_mini_pos, mini_pos);
+	if (!is_sr && n_segs == 1) {
+		for (i = j = 0; i < n_regs0; ++i) {
+			mm_reg1_t *r = &regs0[i];
+			if (r->div > opt->flt_max_dv) continue;
+			if (r->blen < opt->flt_min_blen) continue;
+			regs0[j++] = regs0[i];
+		}
+		n_regs0 = j;
+	}
 
 	if (n_segs == 1) { // uni-segment
 		regs0 = align_regs(opt, mi, b->km, qlens[0], seqs[0], &n_regs0, regs0, a);

minimap.h

@@ -119,6 +119,9 @@ typedef struct {
 	int min_cnt;         // min number of minimizers on each chain
 	int min_chain_score; // min chaining score
 
+	float flt_max_dv;
+	int flt_min_blen;
+
 	float mask_level;
 	float pri_ratio;
 	int best_n;      // top best_n chains are subjected to DP alignment

options.c

@@ -27,6 +27,9 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 	opt->max_chain_skip = 25;
 	opt->max_chain_iter = 5000;
 
+	opt->flt_max_dv = 1.0f;
+	opt->flt_min_blen = 0;
+
 	opt->mask_level = 0.5f;
 	opt->pri_ratio = 0.8f;
 	opt->best_n = 5;