diff --git a/bwa-helper.js b/bwa-helper.js
index 7e938fa..d8477fc 100644
--- a/bwa-helper.js
+++ b/bwa-helper.js
@@ -51,60 +51,6 @@ var getopt = function(args, ostr) {
 	return optopt;
 }
 
-function obj2str(o)
-{
-	if (typeof(o) != 'object') {
-		return o.toString();
-	} else if (o == null) {
-		return "null";
-	} else if (Array.isArray(o)) {
-		var s = "[";
-		for (var i = 0; i < o.length; ++i) {
-			if (i) s += ',';
-			s += obj2str(o[i]);
-		}
-		return s + "]";
-	} else {
-		var i = 0, s = "{";
-		for (var key in o) {
-			if (i++) s += ',';
-			s += key + ":";
-			s += obj2str(o[key]);
-		}
-		return s + "}";
-	}
-}
-
-Bytes.prototype.reverse = function()
-{
-	for (var i = 0; i < this.length>>1; ++i) {
-		var tmp = this[i];
-		this[i] = this[this.length - i - 1];
-		this[this.length - i - 1] = tmp;
-	}
-}
-
-Bytes.prototype.revcomp = function()
-{
-	if (Bytes.rctab == null) {
-		var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
-		var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
-		Bytes.rctab = [];
-		for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
-		for (var i = 0; i < s1.length; ++i)
-			Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
-	}
-	for (var i = 0; i < this.length>>1; ++i) {
-		var tmp = this[this.length - i - 1];
-		this[this.length - i - 1] = Bytes.rctab[this[i]];
-		this[i] = Bytes.rctab[tmp];
-	}
-	if (this.length>>1)
-		this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
-}
-
-var re_cigar = /(\d+)([MIDSHN])/g;
-
 /************************
  *** command markovlp ***
  ************************/
@@ -396,301 +342,6 @@ function bwa_gff2sam(args)
 	file.close();
 }
 
-
-/******************************
- *** Generate ALT alignment ***
- ******************************/
-
-function intv_ovlp(intv, bits) // interval index
-{
-	if (typeof bits == "undefined") bits = 13;
-	intv.sort(function(a,b) {return a[0]-b[0];});
-	// create the index
-	var idx = [], max = 0;
-	for (var i = 0; i < intv.length; ++i) {
-		var b = intv[i][0]>>bits;
-		var e = (intv[i][1]-1)>>bits;
-		if (b != e) {
-			for (var j = b; j <= e; ++j)
-				if (idx[j] == null) idx[j] = i;
-		} else if (idx[b] == null) idx[b] = i;
-		max = max > e? max : e;
-	}
-	// closure
-	return function(_b, _e) {
-		var x = _b >> bits;
-		if (x > max) return [];
-		var off = idx[x];
-		if (off == null) {
-			var i;
-			for (i = ((_e - 1) >> bits) - 1; i >= 0; --i)
-				if (idx[i] != null) break;
-			off = i < 0? 0 : idx[i];
-		}
-		var ovlp = [];
-		for (var i = off; i < intv.length && intv[i][0] < _e; ++i)
-			if (intv[i][1] > _b) ovlp.push(intv[i]);
-		return ovlp;
-	}
-}
-
-function cigar2pos(cigar, pos) // given a pos on ALT and the ALT-to-REF CIGAR, find the pos on REF
-{
-	var x = 0, y = 0;
-	for (var i = 0; i < cigar.length; ++i) {
-		var op = cigar[i][0], len = cigar[i][1];
-		if (op == 'M') {
-			if (y <= pos && pos < y + len)
-				return x + (pos - y);
-			x += len, y += len;
-		} else if (op == 'D') {
-			x += len;
-		} else if (op == 'I') {
-			if (y <= pos && pos < y + len)
-				return x;
-			y += len;
-		} else if (op == 'S' || op == 'H') {
-			if (y <= pos && pos < y + len)
-				return -1;
-			y += len;
-		}
-	}
-	return -1;
-}
-
-function parse_hit(s, opt) // parse a hit. s looks something like ["chr1", "+12345", "100M", 5]
-{
-	var h = {};
-	h.ctg = s[0];
-	h.start = parseInt(s[1].substr(1)) - 1;
-	h.rev = (s[1].charAt(0) == '-');
-	h.cigar = s[2];
-	h.NM = parseInt(s[3]);
-	h.hard = false;
-	var m, l_ins, n_ins, l_del, n_del, l_match, l_skip, l_clip;
-	l_ins = l_del = n_ins = n_del = l_match = l_skip = l_clip = 0;
-	while ((m = re_cigar.exec(h.cigar)) != null) {
-		var l = parseInt(m[1]);
-		if (m[2] == 'M') l_match += l;
-		else if (m[2] == 'D') ++n_del, l_del += l;
-		else if (m[2] == 'I') ++n_ins, l_ins += l;
-		else if (m[2] == 'N') l_skip += l;
-		else if (m[2] == 'H' || m[2] == 'S') {
-			l_clip += l;
-			if (m[2] == 'H') h.hard = true;
-		}
-	}
-	h.end = h.start + l_match + l_del + l_skip;
-	h.NM = h.NM > l_del + l_ins? h.NM : l_del + l_ins;
-	h.score = Math.floor((opt.a * l_match - (opt.a + opt.b) * (h.NM - l_del - l_ins) - opt.o * (n_del + n_ins) - opt.e * (l_del + l_ins)) / opt.a + .499);
-	h.l_query = l_match + l_ins + l_clip;
-	return h;
-}
-
-// read the ALT-to-REF alignment and generate the index
-function read_ALT_sam(fn)
-{
-	var intv = {};
-	var file = new File(fn);
-	var buf = new Bytes();
-	while (file.readline(buf) >= 0) {
-		var line = buf.toString();
-		var t = line.split("\t");
-		if (line.charAt(0) == '@') continue;
-		var flag = parseInt(t[1]);
-		var m, cigar = [], l_qaln = 0, l_qclip = 0;
-		while ((m = re_cigar.exec(t[5])) != null) {
-			var l = parseInt(m[1]);
-			cigar.push([m[2] != 'H'? m[2] : 'S', l]); // convert hard clip to soft clip
-			if (m[2] == 'M' || m[2] == 'I') l_qaln += l;
-			else if (m[2] == 'S' || m[2] == 'H') l_qclip += l;
-		}
-		var j = flag&16? cigar.length-1 : 0;
-		var start = cigar[j][0] == 'S'? cigar[j][1] : 0;
-		if (intv[t[0]] == null) intv[t[0]] = [];
-		intv[t[0]].push([start, start + l_qaln, l_qaln + l_qclip, t[2], flag&16? true : false, parseInt(t[3]) - 1, cigar]);
-		//print(start, start + l_qaln, t[2], flag&16? true : false, parseInt(t[3]), cigar);
-	}
-	buf.destroy();
-	file.close();
-	// create the interval index
-	var idx = {};
-	for (var ctg in intv)
-		idx[ctg] = intv_ovlp(intv[ctg]);
-	return idx;
-}
-
-function bwa_altgen(args)
-{
-	var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false };
-
-	while ((c = getopt(args, 'pv:')) != null) {
-		if (c == 'v') opt.verbose = parseInt(getopt.arg);
-		else if (c == 'p') opt.show_pri = true;
-	}
-
-	if (args.length == getopt.ind) {
-		print("Usage: k8 bwa-helper.js altgen [-p] <alt.sam> [aln.sam]");
-		exit(1);
-	}
-
-	var file, buf = new Bytes();
-	var aux = new Bytes(); // used for reverse and reverse complement
-	var idx = read_ALT_sam(args[getopt.ind]);
-
-	// process SAM
-	file = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : new File();
-	while (file.readline(buf) >= 0) {
-		var m, line = buf.toString();
-		if (line.charAt(0) == '@' || (m = /\tXA:Z:(\S+)/.exec(line)) == null) { // TODO: this does not work with PE file
-			if (opt.verbose < 4) print(line);
-			continue;
-		}
-
-		// parse hits
-		var hits = [];
-		var XA_strs = m[1].split(";");
-		var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
-		var t = line.split("\t");
-		var flag = parseInt(t[1]);
-		var h = parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt);
-		if (h.hard) { // the following does not work with hard clipped SEQ
-			print(line);
-			continue;
-		}
-		hits.push(h);
-		for (var i = 0; i < XA_strs.length; ++i) // hits in the XA tag
-			if (XA_strs[i] != '') // as the last symbol in an XA tag is ";", the last split is an empty string
-				hits.push(parse_hit(XA_strs[i].split(","), opt));
-
-		// lift mapping positions to coordinates on the primary assembly
-		var n_lifted = 0;
-		for (var i = 0; i < hits.length; ++i) {
-			var h = hits[i];
-
-			if (idx[h.ctg] == null) continue;
-			var a = idx[h.ctg](h.start, h.end);
-			if (a == null || a.length == 0) continue;
-
-			// find the approximate position on the primary assembly
-			var lifted = [];
-			for (var j = 0; j < a.length; ++j) {
-				var s, e;
-				if (!a[j][4]) { // ALT is mapped to the forward strand of the primary assembly
-					s = cigar2pos(a[j][6], h.start);
-					e = cigar2pos(a[j][6], h.end - 1) + 1;
-				} else {
-					s = cigar2pos(a[j][6], a[j][2] - h.end);
-					e = cigar2pos(a[j][6], a[j][2] - h.start - 1) + 1;
-				}
-				if (s < 0 || e < 0) continue; // read is mapped to clippings in the ALT-to-chr alignment
-				s += a[j][5]; e += a[j][5];
-				lifted.push([a[j][3], (h.rev!=a[j][4]), s, e]);
-			}
-			if (lifted.length) ++n_lifted, hits[i].lifted = lifted;
-		}
-		if (n_lifted == 0) {
-			if (opt.verbose < 4) print(line);
-			continue;
-		}
-
-		// group hits
-		for (var i = 0; i < hits.length; ++i) { // set keys for sorting
-			if (hits[i].lifted && hits[i].lifted.length) // TODO: only the first element in lifted[] is used
-				hits[i].pctg = hits[i].lifted[0][0], hits[i].pstart = hits[i].lifted[0][2], hits[i].pend = hits[i].lifted[0][3];
-			else hits[i].pctg = hits[i].ctg, hits[i].pstart = hits[i].start, hits[i].pend = hits[i].end;
-			hits[i].i = i; // keep the original index
-		}
-		hits.sort(function(a,b) { return a.pctg != b.pctg? (a.pctg < b.pctg? -1 : 1) : a.pstart - b.pstart });
-		var last_chr = null, end = 0, g = -1;
-		for (var i = 0; i < hits.length; ++i) {
-			if (last_chr != hits[i].pctg) ++g, last_chr = hits[i].pctg, end = 0;
-			else if (hits[i].pstart >= end) ++g;
-			hits[i].g = g;
-			end = end > hits[i].pend? end : hits[i].pend;
-		}
-		var reported_g = null, reported_i = null;
-		for (var i = 0; i < hits.length; ++i)
-			if (hits[i].i == 0)
-				reported_g = hits[i].g, reported_i = i;
-		var n_group0 = 0; // #hits overlapping the reported hit
-		for (var i = 0; i < hits.length; ++i)
-			if (hits[i].g == reported_g)
-				++n_group0;
-		if (n_group0 == 1) { // then keep the reported alignment and mapQ
-			if (opt.verbose < 4) print(line);
-			continue;
-		}
-
-		// re-estimate mapQ
-		var group_max = [];
-		for (var i = 0; i < hits.length; ++i) {
-			var g = hits[i].g;
-			if (group_max[g] == null || group_max[g][0] < hits[i].score)
-				group_max[g] = [hits[i].score, g];
-		}
-		if (group_max.length > 1)
-			group_max.sort(function(x,y) {return y[0]-x[0]});
-		var mapQ;
-		if (group_max[0][1] == reported_g) { // the best hit is the hit reported in SAM
-			mapQ = group_max.length == 1? 60 : 6 * (group_max[0][0] - group_max[1][0]);
-		} else mapQ = 0;
-		mapQ = mapQ < 60? mapQ : 60;
-		var ori_mapQ = parseInt(t[4]);
-		mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ;
-
-		// generate lifted_str
-		for (var i = 0; i < hits.length; ++i) {
-			if (hits[i].lifted && hits[i].lifted.length) {
-				var lifted = hits[i].lifted;
-				var u = '';
-				for (var j = 0; j < lifted.length; ++j)
-					u += lifted[j][0] + "," + lifted[j][2] + "," + lifted[j][3] + "," + (lifted[j][1]?'-':'+') + ";";
-				hits[i].lifted_str = u;
-			}
-		}
-
-		// generate reversed quality and reverse-complemented sequence if necessary
-		var rs = null, rq = null; // reversed quality and reverse complement sequence
-		var need_rev = false;
-		for (var i = 0; i < hits.length; ++i) {
-			if (hits[i].g != reported_g || i == reported_i) continue;
-			if (hits[i].rev != hits[reported_i].rev)
-				need_rev = true;
-		}
-		if (need_rev) { // reverse and reverse complement
-			aux.set(t[9], 0); aux.revcomp(); rs = aux.toString();
-			aux.set(t[10],0); aux.reverse(); rq = aux.toString();
-		}
-
-		// print
-		t[4] = mapQ;
-		t.push("om:i:"+ori_mapQ);
-		if (hits[reported_i].lifted_str) t.push("lt:Z:" + hits[reported_i].lifted_str);
-		print(t.join("\t"));
-		var cnt = 0;
-		for (var i = 0; i < hits.length; ++i) {
-			if (opt.verbose >= 5) print(obj2str(hits[i]));
-			if (hits[i].g != reported_g || i == reported_i) continue;
-			if (!opt.show_pri && idx[hits[i].ctg] == null) continue;
-			var s = [t[0], flag&0xf10, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0];
-			// update name
-			if (flag&0x40) s[0] += "/1";
-			if (flag&0x80) s[0] += "/2";
-			s[0] += "_" + (++cnt);
-			if (hits[i].rev == hits[reported_i].rev) s.push(t[9], t[10]);
-			else s.push(rs, rq);
-			s.push("NM:i:" + hits[i].NM);
-			if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);
-			print(s.join("\t"));
-		}
-	}
-	file.close();
-
-	aux.destroy();
-	buf.destroy();
-}
-
 /*********************
  *** Main function ***
  *********************/
@@ -699,8 +350,7 @@ function main(args)
 {
 	if (args.length == 0) {
 		print("\nUsage:    k8 bwa-helper.js <command> [arguments]\n");
-		print("Commands: altgen       generate ALT alignments for ALT-unaware alignments");
-		print("          sam2pas      convert SAM to pairwise alignment summary format (PAS)");
+		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");
@@ -716,7 +366,6 @@ function main(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 == 'altgen' || cmd == 'genalt') bwa_altgen(args);
 	else if (cmd == 'shortname') bwa_shortname(args);
 	else warn("Unrecognized command");
 }
diff --git a/bwa-postalt.js b/bwa-postalt.js
new file mode 100644
index 0000000..258d25d
--- /dev/null
+++ b/bwa-postalt.js
@@ -0,0 +1,447 @@
+/*****************************************************************
+ * The K8 Javascript interpreter is required to run this script. *
+ *                                                               *
+ *   Source code: https://github.com/attractivechaos/k8          *
+ *   Binary: http://sourceforge.net/projects/lh3/files/k8/       *
+ *                                                               *
+ * Data file used for generating GRCh38 ALT alignments:          *
+ *                                                               *
+ *   http://sourceforge.net/projects/bio-bwa/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;
+}
+
+function obj2str(o)
+{
+	if (typeof(o) != 'object') {
+		return o.toString();
+	} else if (o == null) {
+		return "null";
+	} else if (Array.isArray(o)) {
+		var s = "[";
+		for (var i = 0; i < o.length; ++i) {
+			if (i) s += ',';
+			s += obj2str(o[i]);
+		}
+		return s + "]";
+	} else {
+		var i = 0, s = "{";
+		for (var key in o) {
+			if (i++) s += ',';
+			s += key + ":";
+			s += obj2str(o[key]);
+		}
+		return s + "}";
+	}
+}
+
+Bytes.prototype.reverse = function()
+{
+	for (var i = 0; i < this.length>>1; ++i) {
+		var tmp = this[i];
+		this[i] = this[this.length - i - 1];
+		this[this.length - i - 1] = tmp;
+	}
+}
+
+Bytes.prototype.revcomp = function()
+{
+	if (Bytes.rctab == null) {
+		var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
+		var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
+		Bytes.rctab = [];
+		for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
+		for (var i = 0; i < s1.length; ++i)
+			Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
+	}
+	for (var i = 0; i < this.length>>1; ++i) {
+		var tmp = this[this.length - i - 1];
+		this[this.length - i - 1] = Bytes.rctab[this[i]];
+		this[i] = Bytes.rctab[tmp];
+	}
+	if (this.length>>1)
+		this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
+}
+
+var re_cigar = /(\d+)([MIDSHN])/g;
+
+/******************************
+ *** Generate ALT alignment ***
+ ******************************/
+
+function intv_ovlp(intv, bits) // interval index
+{
+	if (typeof bits == "undefined") bits = 13;
+	intv.sort(function(a,b) {return a[0]-b[0];});
+	// create the index
+	var idx = [], max = 0;
+	for (var i = 0; i < intv.length; ++i) {
+		var b = intv[i][0]>>bits;
+		var e = (intv[i][1]-1)>>bits;
+		if (b != e) {
+			for (var j = b; j <= e; ++j)
+				if (idx[j] == null) idx[j] = i;
+		} else if (idx[b] == null) idx[b] = i;
+		max = max > e? max : e;
+	}
+	// closure
+	return function(_b, _e) {
+		var x = _b >> bits;
+		if (x > max) return [];
+		var off = idx[x];
+		if (off == null) {
+			var i;
+			for (i = ((_e - 1) >> bits) - 1; i >= 0; --i)
+				if (idx[i] != null) break;
+			off = i < 0? 0 : idx[i];
+		}
+		var ovlp = [];
+		for (var i = off; i < intv.length && intv[i][0] < _e; ++i)
+			if (intv[i][1] > _b) ovlp.push(intv[i]);
+		return ovlp;
+	}
+}
+
+function cigar2pos(cigar, pos) // given a pos on ALT and the ALT-to-REF CIGAR, find the pos on REF
+{
+	var x = 0, y = 0;
+	for (var i = 0; i < cigar.length; ++i) {
+		var op = cigar[i][0], len = cigar[i][1];
+		if (op == 'M') {
+			if (y <= pos && pos < y + len)
+				return x + (pos - y);
+			x += len, y += len;
+		} else if (op == 'D') {
+			x += len;
+		} else if (op == 'I') {
+			if (y <= pos && pos < y + len)
+				return x;
+			y += len;
+		} else if (op == 'S' || op == 'H') {
+			if (y <= pos && pos < y + len)
+				return -1;
+			y += len;
+		}
+	}
+	return -1;
+}
+
+function parse_hit(s, opt) // parse a hit. s looks something like ["chr1", "+12345", "100M", 5]
+{
+	var h = {};
+	h.ctg = s[0];
+	h.start = parseInt(s[1].substr(1)) - 1;
+	h.rev = (s[1].charAt(0) == '-');
+	h.cigar = s[2];
+	h.NM = parseInt(s[3]);
+	h.hard = false;
+	var m, l_ins, n_ins, l_del, n_del, l_match, l_skip, l_clip;
+	l_ins = l_del = n_ins = n_del = l_match = l_skip = l_clip = 0;
+	while ((m = re_cigar.exec(h.cigar)) != null) {
+		var l = parseInt(m[1]);
+		if (m[2] == 'M') l_match += l;
+		else if (m[2] == 'D') ++n_del, l_del += l;
+		else if (m[2] == 'I') ++n_ins, l_ins += l;
+		else if (m[2] == 'N') l_skip += l;
+		else if (m[2] == 'H' || m[2] == 'S') {
+			l_clip += l;
+			if (m[2] == 'H') h.hard = true;
+		}
+	}
+	h.end = h.start + l_match + l_del + l_skip;
+	h.NM = h.NM > l_del + l_ins? h.NM : l_del + l_ins;
+	h.score = Math.floor((opt.a * l_match - (opt.a + opt.b) * (h.NM - l_del - l_ins) - opt.o * (n_del + n_ins) - opt.e * (l_del + l_ins)) / opt.a + .499);
+	h.l_query = l_match + l_ins + l_clip;
+	return h;
+}
+
+// read the ALT-to-REF alignment and generate the index
+function read_ALT_sam(fn)
+{
+	var intv = {};
+	var file = new File(fn);
+	var buf = new Bytes();
+	while (file.readline(buf) >= 0) {
+		var line = buf.toString();
+		var t = line.split("\t");
+		if (line.charAt(0) == '@') continue;
+		var flag = parseInt(t[1]);
+		var m, cigar = [], l_qaln = 0, l_qclip = 0;
+		while ((m = re_cigar.exec(t[5])) != null) {
+			var l = parseInt(m[1]);
+			cigar.push([m[2] != 'H'? m[2] : 'S', l]); // convert hard clip to soft clip
+			if (m[2] == 'M' || m[2] == 'I') l_qaln += l;
+			else if (m[2] == 'S' || m[2] == 'H') l_qclip += l;
+		}
+		var j = flag&16? cigar.length-1 : 0;
+		var start = cigar[j][0] == 'S'? cigar[j][1] : 0;
+		if (intv[t[0]] == null) intv[t[0]] = [];
+		intv[t[0]].push([start, start + l_qaln, l_qaln + l_qclip, t[2], flag&16? true : false, parseInt(t[3]) - 1, cigar]);
+		//print(start, start + l_qaln, t[2], flag&16? true : false, parseInt(t[3]), cigar);
+	}
+	buf.destroy();
+	file.close();
+	// create the interval index
+	var idx = {};
+	for (var ctg in intv)
+		idx[ctg] = intv_ovlp(intv[ctg]);
+	return idx;
+}
+
+function bwa_postalt(args)
+{
+	var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false, recover_mapq:true };
+
+	while ((c = getopt(args, 'pqv:')) != null) {
+		if (c == 'v') opt.verbose = parseInt(getopt.arg);
+		else if (c == 'p') opt.show_pri = true;
+		else if (c == 'q') opt.recover_maq = false;
+	}
+
+	if (args.length == getopt.ind) {
+		print("");
+		print("Usage:   k8 bwa-postalt.js [-p] <alt.sam> [aln.sam]\n");
+		print("Options: -p    output lifted non-ALT hit in a SAM line (for ALT-unware alignments)");
+		print("         -q    don't recover mapQ for non-ALTs hit overlapping lifted ALT");
+		print("");
+		print("Note: This script inspects the XA tag, lifts the mapping positions of ALT hits to");
+		print("      the primary assembly, groups them and then estimates mapQ across groups. If");
+		print("      a non-ALT hit overlaps a lifted ALT hit, its mapping quality is set to the");
+		print("      smaller between its original mapQ and the adjusted mapQ of the ALT hit. If");
+		print("      multiple ALT hits are lifted to the same position, they will yield new SAM");
+		print("      lines with the same mapQ.");
+		print("");
+		exit(1);
+	}
+
+	var file, buf = new Bytes();
+	var aux = new Bytes(); // used for reverse and reverse complement
+	var idx = read_ALT_sam(args[getopt.ind]);
+	var buf2 = [];
+
+	// process SAM
+	file = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : new File();
+	while (file.readline(buf) >= 0) {
+		var m, line = buf.toString();
+		if (line.charAt(0) == '@') { // print and then skip the header line
+			print(line);
+			continue;
+		}
+
+		var t = line.split("\t");
+		t[1] = parseInt(t[1]); t[3] = parseInt(t[3]); t[4] = parseInt(t[4]);
+		if (buf2.length && buf2[0][0] != t[0]) {
+			for (var i = 0; i < buf2.length; ++i)
+				print(buf2[i].join("\t"));
+			buf2 = [];
+		}
+
+		if ((m = /\tXA:Z:(\S+)/.exec(line)) == null) { // TODO: this does not work with PE file
+			buf2.push(t);
+			continue;
+		}
+
+		// parse hits
+		var hits = [];
+		var XA_strs = m[1].split(";");
+		var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
+		var flag = t[1];
+		var h = parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt);
+		if (h.hard) { // don't process lines with hard clips
+			buf2.push(t);
+			continue;
+		}
+		hits.push(h);
+		for (var i = 0; i < XA_strs.length; ++i) // hits in the XA tag
+			if (XA_strs[i] != '') // as the last symbol in an XA tag is ";", the last split is an empty string
+				hits.push(parse_hit(XA_strs[i].split(","), opt));
+
+		// lift mapping positions to coordinates on the primary assembly
+		var n_lifted = 0, n_rpt_lifted = 0;
+		for (var i = 0; i < hits.length; ++i) {
+			var h = hits[i];
+
+			if (idx[h.ctg] == null) continue;
+			var a = idx[h.ctg](h.start, h.end);
+			if (a == null || a.length == 0) continue;
+
+			// find the approximate position on the primary assembly
+			var lifted = [];
+			for (var j = 0; j < a.length; ++j) {
+				var s, e;
+				if (!a[j][4]) { // ALT is mapped to the forward strand of the primary assembly
+					s = cigar2pos(a[j][6], h.start);
+					e = cigar2pos(a[j][6], h.end - 1) + 1;
+				} else {
+					s = cigar2pos(a[j][6], a[j][2] - h.end);
+					e = cigar2pos(a[j][6], a[j][2] - h.start - 1) + 1;
+				}
+				if (s < 0 || e < 0) continue; // read is mapped to clippings in the ALT-to-chr alignment
+				s += a[j][5]; e += a[j][5];
+				lifted.push([a[j][3], (h.rev!=a[j][4]), s, e]);
+				if (i == 0) ++n_rpt_lifted;
+			}
+			if (lifted.length) ++n_lifted, hits[i].lifted = lifted;
+		}
+		if (n_lifted == 0) {
+			buf2.push(t);
+			continue;
+		}
+
+		// group hits
+		for (var i = 0; i < hits.length; ++i) { // set keys for sorting
+			if (hits[i].lifted && hits[i].lifted.length) // TODO: only the first element in lifted[] is used
+				hits[i].pctg = hits[i].lifted[0][0], hits[i].pstart = hits[i].lifted[0][2], hits[i].pend = hits[i].lifted[0][3];
+			else hits[i].pctg = hits[i].ctg, hits[i].pstart = hits[i].start, hits[i].pend = hits[i].end;
+			hits[i].i = i; // keep the original index
+		}
+		hits.sort(function(a,b) { return a.pctg != b.pctg? (a.pctg < b.pctg? -1 : 1) : a.pstart - b.pstart });
+		var last_chr = null, end = 0, g = -1;
+		for (var i = 0; i < hits.length; ++i) {
+			if (last_chr != hits[i].pctg) ++g, last_chr = hits[i].pctg, end = 0;
+			else if (hits[i].pstart >= end) ++g;
+			hits[i].g = g;
+			end = end > hits[i].pend? end : hits[i].pend;
+		}
+		var reported_g = null, reported_i = null;
+		for (var i = 0; i < hits.length; ++i)
+			if (hits[i].i == 0)
+				reported_g = hits[i].g, reported_i = i;
+		var n_group0 = 0; // #hits overlapping the reported hit
+		for (var i = 0; i < hits.length; ++i)
+			if (hits[i].g == reported_g)
+				++n_group0;
+
+		var mapQ, ori_mapQ = t[4];
+		if (n_group0 > 1) { // then re-estimate mapQ
+			var group_max = [];
+			for (var i = 0; i < hits.length; ++i) {
+				var g = hits[i].g;
+				if (group_max[g] == null || group_max[g][0] < hits[i].score)
+					group_max[g] = [hits[i].score, g];
+			}
+			if (group_max.length > 1)
+				group_max.sort(function(x,y) {return y[0]-x[0]});
+			if (group_max[0][1] == reported_g) { // the best hit is the hit reported in SAM
+				mapQ = group_max.length == 1? 60 : 6 * (group_max[0][0] - group_max[1][0]);
+			} else mapQ = 0;
+			mapQ = mapQ < 60? mapQ : 60;
+			mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ;
+		} else mapQ = t[4];
+
+		// check if the reported hit overlaps a hit to the primary assembly; if so, don't reduce mapping quality
+		if (opt.recover_mapq && n_rpt_lifted == 1 && mapQ > 0) {
+			var l = lifted[0];
+			for (var i = 0; i < buf2.length; ++i) {
+				var s = buf2[i];
+				if (l[0] != s[2]) continue; // different chr
+				if (((s[1]&16) != 0) != l[1]) continue; // different strand
+				var start = s[3] - 1, end = start;
+				while ((m = re_cigar.exec(t[5])) != null)
+					if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N')
+						end += parseInt(m[1]);
+				if (start < l[3] && l[2] < end) {
+					var om = -1;
+					for (var j = 11; j < s.length; ++j)
+						if ((m = /^om:i:(\d+)/.exec(s[j])) != null)
+							om = parseInt(m[1]);
+					if (om > 0) s[4] = om;
+					s[4] = s[4] < mapQ? s[4] : mapQ;
+				}
+			}
+		}
+
+		// generate lifted_str
+		for (var i = 0; i < hits.length; ++i) {
+			if (hits[i].lifted && hits[i].lifted.length) {
+				var u = '', lifted = hits[i].lifted;
+				for (var j = 0; j < lifted.length; ++j)
+					u += lifted[j][0] + "," + lifted[j][2] + "," + lifted[j][3] + "," + (lifted[j][1]?'-':'+') + ";";
+				hits[i].lifted_str = u;
+			}
+		}
+
+		// generate reversed quality and reverse-complemented sequence if necessary
+		var rs = null, rq = null; // reversed quality and reverse complement sequence
+		var need_rev = false;
+		for (var i = 0; i < hits.length; ++i) {
+			if (hits[i].g != reported_g || i == reported_i) continue;
+			if (hits[i].rev != hits[reported_i].rev)
+				need_rev = true;
+		}
+		if (need_rev) { // reverse and reverse complement
+			aux.set(t[9], 0); aux.revcomp(); rs = aux.toString();
+			aux.set(t[10],0); aux.reverse(); rq = aux.toString();
+		}
+
+		// print
+		t[4] = mapQ;
+		if (n_group0 > 1) t.push("om:i:"+ori_mapQ);
+		if (hits[reported_i].lifted_str) t.push("lt:Z:" + hits[reported_i].lifted_str);
+		buf2.push(t);
+		var cnt = 0;
+		for (var i = 0; i < hits.length; ++i) {
+			if (opt.verbose >= 5) print(obj2str(hits[i]));
+			if (hits[i].g != reported_g || i == reported_i) continue;
+			if (!opt.show_pri && idx[hits[i].ctg] == null) continue;
+			var s = [t[0], flag&0xf10, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0];
+			// update name
+			if (flag&0x40) s[0] += "/1";
+			if (flag&0x80) s[0] += "/2";
+			s[0] += "_" + (++cnt);
+			if (hits[i].rev == hits[reported_i].rev) s.push(t[9], t[10]);
+			else s.push(rs, rq);
+			s.push("NM:i:" + hits[i].NM);
+			if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);
+			buf2.push(s);
+		}
+	}
+	for (var i = 0; i < buf2.length; ++i)
+		print(buf2[i].join("\t"));
+	file.close();
+
+	aux.destroy();
+	buf.destroy();
+}
+
+bwa_postalt(arguments);