diff --git a/misc/splice2bed.js b/misc/splice2bed.js
new file mode 100644
index 0000000..241d547
--- /dev/null
+++ b/misc/splice2bed.js
@@ -0,0 +1,125 @@
+var getopt = function(args, ostr) {
+	var oli; // option letter list index
+	if (typeof(getopt.place) == 'undefined')
+		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
+	if (getopt.place == -1) { // update scanning pointer
+		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
+			getopt.place = -1;
+			return null;
+		}
+		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
+			++getopt.ind;
+			getopt.place = -1;
+			return null;
+		}
+	}
+	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
+	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
+		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
+		if (getopt.place < 0) ++getopt.ind;
+		return '?';
+	}
+	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
+		getopt.arg = null;
+		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
+	} else { // need an argument
+		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
+			getopt.arg = args[getopt.ind].substr(getopt.place);
+		else if (args.length <= ++getopt.ind) { // no arg
+			getopt.place = -1;
+			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
+			return '?';
+		} else getopt.arg = args[getopt.ind]; // white space
+		getopt.place = -1;
+		++getopt.ind;
+	}
+	return optopt;
+}
+
+var colors = ["0,128,255", "255,0,0", "0,192,0"];
+
+function print_lines(a, fmt) {
+	if (a.length == 0) return;
+	if (fmt == "bed") {
+		var n_pri = 0;
+		for (var i = 0; i < a.length; ++i)
+			if (a[i][9] == 0) ++n_pri;
+		if (n_pri > 1) {
+			for (var i = 0; i < a.length; ++i)
+				if (a[i][9] == 0) a[i][9] = 1;
+		} else if (n_pri == 0) {
+			warn("Warning: " + a[0][0] + " doesn't have a primary alignment");
+		}
+		for (var i = 0; i < a.length; ++i) {
+			a[i][9] = colors[a[i][9]];
+			a[i].shift();
+			print(a[i].join("\t"));
+		}
+	}
+	a.length = 0;
+}
+
+function main(args) {
+	var re = /(\d+)([MIDNSH])/g;
+	var c, fmt = "bed", with_hdr = false, hdr_only = false, name = 'splice2bed', pos = null;
+	while ((c = getopt(args, "Hhn:p:")) != null) {
+		if (c == 'h') with_hdr = true;
+		else if (c == 'p') pos = getopt.arg;
+		else if (c == 'H') with_hdr = hdr_only = true;
+		else if (c == 'n') name = getopt.arg;
+	}
+	if (getopt.ind == args.length && !hdr_only) {
+		warn("Usage: k8 splice2bed.js [options] <in.paf>");
+		exit(1);
+	}
+	if (with_hdr) {
+		if (pos != null)
+			print('browser position ' + pos);
+		print('track name=' + name + ' useScore=1 visibility=2 itemRgb="On"');
+	}
+	if (hdr_only) return;
+	var file = new File(args[getopt.ind]);
+	var buf = new Bytes();
+	var a = [];
+	while (file.readline(buf) >= 0) {
+		var line = buf.toString();
+		if (line.charAt(0) == '@') continue; // skip SAM header lines
+		var t = line.split("\t");
+		if (t.length >= 12 && (t[4] == '+' || t[4] == '-')) {
+			if (a.length && a[0][0] != t[0]) {
+				print_lines(a, fmt);
+				a = [];
+			}
+			var is_pri = false, cigar = null;
+			for (var i = 12; i < t.length; ++i) {
+				if (t[i].substr(0, 5) == 'cg:Z:') {
+					cigar = t[i].substr(5);
+				} else if (t[i].substr(0, 5) == 's2:i:') {
+					is_pri = true;
+				}
+			}
+			if (cigar == null) throw Error("missing CIGAR");
+			var m, x0 = 0, x = 0, bs = [], bl = [];
+			while ((m = re.exec(cigar)) != null) {
+				if (m[2] == 'M' || m[2] == 'D') {
+					x += parseInt(m[1]);
+				} else if (m[2] == 'N') {
+					bs.push(x0);
+					bl.push(x - x0);
+					x += parseInt(m[1]);
+					x0 = x;
+				}
+			}
+			bs.push(x0);
+			bl.push(x - x0);
+			a.push([t[0], t[5], t[7], t[8], t[0], Math.floor(t[9]/t[10]*1000), t[4], t[7], t[8], is_pri? 0:2, bs.length, bl.join(",")+",", bs.join(",")+","]);
+		} else {
+			throw Error("unrecognized input format");
+		}
+	}
+	print_lines(a, fmt);
+	buf.destroy();
+	file.close();
+}
+
+main(arguments);