diff --git a/bwa-helper.js b/bwa-helper.js
new file mode 100644
index 0000000..e904fc2
--- /dev/null
+++ b/bwa-helper.js
@@ -0,0 +1,369 @@
+/*****************************************************************
+ * The K8 Javascript interpreter is required to run this script. *
+ *                                                               *
+ *   Source code: https://github.com/attractivechaos/k8          *
+ *   Binary: https://sourceforge.net/projects/lh3/files/         *
+ *****************************************************************/
+
+/******************
+ *** From k8.js ***
+ ******************/
+
+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;
+}
+
+/************************
+ *** command markovlp ***
+ ************************/
+
+function bwa_markOvlp(args)
+{
+	var c, min_aln_ratio = .9, min_ext = 50;
+	while ((c = getopt(args, "r:e:")) != null) {
+		if (c == 'r') min_aln_ratio = parseFloat(getopt.arg);
+		else if (c == 'e') min_ext = parseInt(getopt.arg);
+	}
+
+	var file = args.length == getopt.ind? new File() : new File(args[getopt.ind]);
+	var buf = new Bytes();
+	var dir4 = ['>>', '><', '<>', '<<'];
+
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t")
+			for (var i = 0; i < t.length; ++i)
+				if (i != 0 && i != 4)
+					t[i] = parseInt(t[i]);
+		var el, a1, a2, e1, e2, r1, r2; // a: aligned length; e: extended length; r: remaining length
+		e2 = a2 = t[7] - t[6];
+		if (t[2] < t[3]) { // forward-forward match
+			e1 = a1 = t[3] - t[2];
+			r1 = t[2] - t[6];
+			r2 = (t[5] - t[7]) - (t[1] - t[3]);
+			el = r1 > 0? t[6] : t[2];
+			el += r2 > 0? t[1] - t[3] : t[5] - t[7];
+		} else { // reverse-forward match
+			e1 = a1 = t[2] - t[3];
+			r1 = (t[1] - t[2]) - t[6];
+			r2 = (t[5] - t[7]) - t[3];
+			el = r1 > 0? t[6] : t[1] - t[2];
+			el += r2 > 0? t[3] : t[5] - t[7];
+		}
+		e1 += el; e2 += el;
+		var type;
+		if (a1 / e1 >= min_aln_ratio && a2 / e2 >= min_aln_ratio) {
+			if ((r1 >= min_ext && r2 >= min_ext) || (r1 <= -min_ext && r2 <= -min_ext)) { // suffix-prefix match
+				var d = t[2] < t[3]? 0 : 2;
+				if (r1 < 0) d ^= 3; // reverse the direction
+				type = 'O' + dir4[d];
+			} else type = 'C' + (e1 / t[1] > e2 / t[5]? 1 : 2);
+		} else type = 'I'; // internal local match; not a suffix-prefix match
+		//print(t[1], e1, a1, t[5], e2, a2);
+		print(type, buf);
+	}
+
+	buf.destroy();
+	file.close();
+}
+
+/***********************
+ *** command pas2bed ***
+ ***********************/
+
+function bwa_pas2reg(args)
+{
+	var file = args.length? new File(args[0]) : new File();
+	var buf = new Bytes();
+
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t");
+		if (t[0] == t[4]) continue;
+		if (parseInt(t[2]) < parseInt(t[3])) print(t[0], t[1], t[2], t[3], t[8]);
+		else print(t[0], t[1], t[3], t[2], t[8]);
+		print(t[4], t[5], t[6], t[7], t[8]);
+	}
+
+	buf.destroy();
+	file.close();
+}
+
+/*******************
+ * command sam2pas *
+ *******************/
+
+function bwa_sam2pas(args)
+{
+	var file = args.length == 0? new File() : new File(args[0]);
+	var buf = new Bytes();
+	var seq_dict = {};
+
+	while (file.readline(buf) >= 0) {
+		var line = buf.toString();
+		var m;
+		if (/^@SQ/.test(line)) {
+			var name = null, len = null;
+			if ((m = /\tSN:(\S+)/.exec(line)) != null) name = m[1];
+			if ((m = /\tLN:(\S+)/.exec(line)) != null) len = parseInt(m[1]);
+			if (name != null && len != null) seq_dict[name] = len;
+		}
+		if (/^@/.test(line)) continue;
+		var t = line.split("\t");
+		var pos = parseInt(t[3]) - 1;
+		var x = 0, y = 0, i = 0, clip = [0, 0], n_ins = 0, n_del = 0, o_ins = 0, o_del = 0, n_M = 0;
+		var re = /(\d+)([MIDSH])/g;
+		while ((m = re.exec(t[5])) != null) {
+			var l = parseInt(m[1]);
+			if (m[2] == 'M') x += l, y += l, n_M += l;
+			else if (m[2] == 'I') y += l, n_ins += l, ++o_ins;
+			else if (m[2] == 'D') x += l, n_del += l, ++o_del;
+			else if (m[2] == 'S' || m[2] == 'H')
+				clip[i == 0? 0 : 1] = l;
+			++i;
+		}
+		var is_rev = (parseInt(t[1]) & 16)? true : false;
+		var misc = 'mapQ=' + t[4] + ';';
+		var usc = 1;
+		if ((m = /\tNM:i:(\d+)/.exec(line)) != null) {
+			var NM = parseInt(m[1]);
+			var diff = (NM / (n_M + n_ins + n_del)).toFixed(3);
+			misc += 'diff=' + diff + ';n_mis=' + (NM - n_del - n_ins) + ';';
+		}
+		misc += 'n_del='+n_del+';n_ins='+n_ins+';o_del='+o_del+';o_ins='+o_ins + ';';
+		if ((m = /\tAS:i:(\d+)/.exec(line)) != null) {
+			misc += 'AS='+m[1] + ';';
+			usc = (parseInt(m[1]) / (x > y? x : y)).toFixed(3);
+		}
+		if ((m = /\tXS:i:(\d+)/.exec(line)) != null) misc += 'XS='+m[1] + ';';
+		var len = y + clip[0] + clip[1];
+		var z = [t[0], len, clip[0], clip[0] + y, t[2], seq_dict[t[2]], pos, pos + x, usc, misc];
+		if (parseInt(t[1]) & 16) z[2] = clip[1] + y, z[3] = clip[1];
+		print(z.join("\t"));
+	}
+
+	buf.destroy();
+	file.close();
+}
+
+/***********************
+ *** command reg2cut ***
+ ***********************/
+
+function bwa_reg2cut(args)
+{
+	var c, min_usc = 0.5, min_ext = 100, min_len = 5000, cut = 250;
+	while ((c = getopt(args, "s:e:l:c:")) != null) {
+		if (c == 's') min_usc = parseFloat(getopt.arg);
+		else if (c == 'e') min_ext = parseInt(getopt.arg);
+		else if (c == 'l') min_len = parseInt(getopt.arg);
+		else if (c == 'c') cut = parseInt(getopt.arg);
+	}
+
+	var file = args.length == getopt.ind? new File () : new File(args[getopt.ind]);
+	var buf = new Bytes();
+
+	function print_bed() {
+		for (var i = 0; i < a.length; ++i) {
+			var start = a[i][0] - cut > 0? a[i][0] : 0;
+			var end   = a[i][1] + cut < last_len? a[i][1] : last_len;
+			if (end - start >= min_len) print(last_chr, start, end);
+		}
+	}
+
+	var last_chr = null, last_len = null, max_c_usc = 0, start = 0, end = 0;
+	var a = [];
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split("\t");
+		t[1] = parseInt(t[1]);
+		t[2] = parseInt(t[2]);
+		t[3] = parseInt(t[3]);
+		t[4] = parseFloat(t[4]);
+		var is_contained = t[2] < min_ext && t[1] - t[3] < min_ext? true : false;
+		if (t[3] - t[2] < cut<<1) continue;
+		t[2] += cut; t[3] -= cut;
+		if (t[0] != last_chr) {
+			a.push([start, end]);
+			if (last_chr != null && max_c_usc < min_usc) print_bed();
+			last_chr = t[0]; last_len = t[1]; start = t[2]; end = t[3];
+			max_c_usc = is_contained? t[4] : 0;
+			a.length = 0;
+		} else {
+			if (is_contained)
+				max_c_usc = max_c_usc > t[4]? max_c_usc : t[4];
+			if (t[4] < min_usc) continue;
+			if (t[2] > end) {
+				a.push([start, end]);
+				start = t[2];
+				end = end > t[3]? end : t[3];
+			} else end = end > t[3]? end : t[3];
+		}
+	}
+	a.push([start, end]);
+	if (max_c_usc < min_usc) print_bed(); // the last sequence
+
+	buf.destroy();
+	file.close();
+}
+
+function bwa_shortname(args)
+{
+	var file = args.length? new File(args[0]) : new File();
+	var buf = new Bytes();
+
+	var re = /(\S+)\/(\d+)_(\d+)((:\d+-\d+)+)/g;
+	var re2 = /:(\d+)-(\d+)/g;
+	while (file.readline(buf) >= 0) {
+		var match, match2;
+		var line = buf.toString();
+		var x = [];
+		while ((match = re.exec(line)) != null) {
+			var start = parseInt(match[2]), len = parseInt(match[3]) - start;
+			while ((match2 = re2.exec(match[4])) != null) {
+				var a = parseInt(match2[1]) - 1;
+				var b = parseInt(match2[2]);
+				start += a; len = b - a;
+			}
+			x.push([match[0], match[1] + '/' + start.toString() + '_' + (start+len).toString()]);
+		}
+		for (var i = 0; i < x.length; ++i)
+			line = line.replace(x[i][0], x[i][1]);
+		print(line);
+	}
+
+	buf.destroy();
+	file.close();
+}
+
+/*******************
+ * Command gff2sam *
+ *******************/
+
+function bwa_gff2sam(args)
+{
+	if (args.length < 2) {
+		print("Usage: k8 bwa-helper.js <aln.gff> <query-length.txt>");
+		exit(1);
+	}
+
+	var file = new File(args[1]);
+	var buf = new Bytes();
+	var len = {};
+
+	while (file.readline(buf) >= 0) {
+		var t = buf.toString().split(/\s+/);
+		len[t[0]] = parseInt(t[1]);
+	}
+	file.close();
+
+	file = new File(args[0]);
+	var re_cigar = /([MID])(\d+)/g;
+	var lineno = 0;
+	while (file.readline(buf) >= 0) {
+		++lineno;
+		var t = buf.toString().split("\t");
+		var m = /Target=(\S+)\s+(\d+)\s+(\d+)\s+([+-])/.exec(t[8]);
+		if (m == null) {
+			warn("WARNING: skipped line "+lineno+" due to the lack of Target.");
+			continue;
+		}
+		var qname = m[1];
+		var flag = t[6] == m[4]? 0 : 16;
+		var qb = parseInt(m[2]) - 1, qe = parseInt(m[3]), qlen = len[qname];
+		if (qlen == null)
+			throw Error("Sequence "+qname+" is not present in the query-length.txt");
+		var clip5 = qb, clip3 = qlen - qe;
+		if (flag&16) clip5 ^= clip3, clip3 ^= clip5, clip5 ^= clip3; // swap
+
+		m = /Gap\s*=\s*(([MID]\d+\s*)+)/.exec(t[8]);
+		var cigar = clip5? clip5 + 'S' : '';
+		var n_ins = 0, n_del = 0, n_match = 0, NM = null;
+		if (m) {
+			var mc;
+			while ((mc = re_cigar.exec(m[1])) != null) {
+				var l = parseInt(mc[2]);
+				cigar += mc[2] + mc[1];
+				if (mc[1] == 'I') n_ins += l;
+				else if (mc[1] == 'D') n_del += l;
+				else if (mc[1] == 'M') n_match += l;
+			}
+			if (n_ins + n_match != qe - qb || n_del + n_match != parseInt(t[4]) - parseInt(t[3]) + 1)
+				throw Error("Inconsistent CIGAR at line "+lineno);
+		} else { // ungapped alignment
+			var tb = parseInt(t[3]) - 1, te = parseInt(t[4]);
+			if (te - tb != qe - qb) {
+				warn("WARNING: line "+lineno+" should contain gaps, but lacks Gap. Skipped.\n");
+			} else cigar = (qe - qb) + 'M';
+		}
+		if (clip3) cigar += clip3 + 'S';
+		if ((m = /num_mismatch=(\d+)/.exec(t[8])) != null)
+			NM = parseInt(m[1]) + n_ins + n_del;
+		var out = [qname, flag, t[0], t[3], 255, cigar, '*', 0, 0, '*', '*'];
+		if (NM != null) out.push('NM:i:' + NM);
+		print(out.join("\t"));
+	}
+	buf.destroy();
+	file.close();
+}
+
+/*********************
+ *** Main function ***
+ *********************/
+
+function main(args)
+{
+	if (args.length == 0) {
+		print("\nUsage:    k8 bwa-helper.js <command> [arguments]\n");
+		print("Commands: sam2pas      convert SAM to pairwise alignment summary format (PAS)");
+		print("          pas2reg      extract covered regions");
+		print("          reg2cut      regions to extract for the 2nd round bwa-mem");
+		print("          markovlp     identify bi-directional overlaps");
+		print("          gff2sam      convert GFF3 alignment to SAM");
+		print("          shortname    shorten sequence name after subseq (PacBio read names only)");
+		print("");
+		exit(1);
+	}
+
+	var cmd = args.shift();
+	if (cmd == 'sam2pas') bwa_sam2pas(args);
+	else if (cmd == 'gff2sam') bwa_gff2sam(args);
+	else if (cmd == 'markovlp') bwa_markOvlp(args);
+	else if (cmd == 'pas2reg') bwa_pas2reg(args);
+	else if (cmd == 'reg2cut') bwa_reg2cut(args);
+	else if (cmd == 'shortname') bwa_shortname(args);
+	else warn("Unrecognized command");
+}
+
+main(arguments);