BED I/O

main.c

@@ -63,6 +63,8 @@ static ko_longopt_t long_options[] = {
 	{ "cap-sw-mem",     ko_required_argument, 337 },
 	{ "max-qlen",       ko_required_argument, 338 },
 	{ "max-chain-iter", ko_required_argument, 339 },
+	{ "junc-bed",       ko_required_argument, 340 },
+	{ "junc-bonus",     ko_required_argument, 341 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -105,7 +107,7 @@ int main(int argc, char *argv[])
 	mm_mapopt_t opt;
 	mm_idxopt_t ipt;
 	int i, c, n_threads = 3, n_parts, old_best_n = -1;
-	char *fnw = 0, *rg = 0, *s;
+	char *fnw = 0, *rg = 0, *junc_bed = 0, *s;
 	FILE *fp_help = stderr;
 	mm_idx_reader_t *idx_rdr;
 	mm_idx_t *mi;
@@ -204,6 +206,7 @@ int main(int argc, char *argv[])
 		else if (c == 336) opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level
 		else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
 		else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
+		else if (c == 339) junc_bed = o.arg; // --junc-bed
 		else if (c == 314) { // --frag
 			yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
 		} else if (c == 315) { // --secondary
@@ -343,6 +346,7 @@ int main(int argc, char *argv[])
 	if (opt.best_n == 0 && (opt.flag&MM_F_CIGAR) && mm_verbose >= 2)
 		fprintf(stderr, "[WARNING]\033[1;31m `-N 0' reduces alignment accuracy. Please use --secondary=no to suppress secondary alignments.\033[0m\n");
 	while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
+		if (junc_bed) mm_idx_bed_read(mi, junc_bed);
 		if ((opt.flag & MM_F_CIGAR) && (mi->flag & MM_I_NO_SEQ)) {
 			fprintf(stderr, "[ERROR] the prebuilt index doesn't contain sequences.\n");
 			mm_idx_destroy(mi);