paftools.js

#!/usr/bin/env k8

var paftools_version = 'r767';

/*****************************
 ***** Library functions *****
 *****************************/

/*******************************
 * Command line option parsing *
 *******************************/

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;
}

/***********************
 * Interval operations *
 ***********************/

Interval = {};

Interval.sort = function(a)
{
	if (typeof a[0] == 'number')
		a.sort(function(x, y) { return x - y });
	else a.sort(function(x, y) { return x[0] != y[0]? x[0] - y[0] : x[1] - y[1] });
}

Interval.merge = function(a, sorted)
{
	if (typeof sorted == 'undefined') sorted = true;
	if (!sorted) Interval.sort(a);
	var k = 0;
	for (var i = 1; i < a.length; ++i) {
		if (a[k][1] >= a[i][0])
			a[k][1] = a[k][1] > a[i][1]? a[k][1] : a[i][1];
		else a[++k] = a[i].slice(0);
	}
	a.length = k + 1;
}

Interval.index_end = function(a, sorted)
{
	if (a.length == 0) return;
	if (typeof sorted == 'undefined') sorted = true;
	if (!sorted) Interval.sort(a);
	a[0].push(0);
	var k = 0, k_en = a[0][1];
	for (var i = 1; i < a.length; ++i) {
		if (k_en <= a[i][0]) {
			for (++k; k < i; ++k)
				if (a[k][1] > a[i][0])
					break;
			k_en = a[k][1];
		}
		a[i].push(k);
	}
}

Interval.find_intv = function(a, x)
{
	var left = -1, right = a.length;
	if (typeof a[0] == 'number') {
		while (right - left > 1) {
			var mid = left + ((right - left) >> 1);
			if (a[mid] > x) right = mid;
			else if (a[mid] < x) left = mid;
			else return mid;
		}
	} else {
		while (right - left > 1) {
			var mid = left + ((right - left) >> 1);
			if (a[mid][0] > x) right = mid;
			else if (a[mid][0] < x) left = mid;
			else return mid;
		}
	}
	return left;
}

Interval.find_ovlp = function(a, st, en)
{
	if (a.length == 0 || st >= en) return [];
	var l = Interval.find_intv(a, st);
	var k = l < 0? 0 : a[l][a[l].length - 1];
	var b = [];
	for (var i = k; i < a.length; ++i) {
		if (a[i][0] >= en) break;
		else if (st < a[i][1])
			b.push(a[i]);
	}
	return b;
}

/**********************************
 * Reverse and reverse complement *
 **********************************/

function fasta_read(fn)
{
	var h = {}, gt = '>'.charCodeAt(0);
	var file = fn == '-'? new File() : new File(fn);
	var buf = new Bytes(), seq = null, name = null, seqlen = [];
	while (file.readline(buf) >= 0) {
		if (buf[0] == gt) {
			if (seq != null && name != null) {
				seqlen.push([name, seq.length]);
				h[name] = seq;
				name = seq = null;
			}
			var m, line = buf.toString();
			if ((m = /^>(\S+)/.exec(line)) != null) {
				name = m[1];
				seq = new Bytes();
			}
		} else seq.set(buf);
	}
	if (seq != null && name != null) {
		seqlen.push([name, seq.length]);
		h[name] = seq;
	}
	buf.destroy();
	file.close();
	return [h, seqlen];
}

function fasta_free(fa)
{
	for (var name in fa)
		fa[name].destroy();
}

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;
	}
}

// reverse complement a DNA string
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]];
}

/********************
 ***** paftools *****
 ********************/

/*****************
 * Miscellaneous *
 *****************/

// liftover
function paf_liftover(args)
{
	function read_bed(fn, to_merge)
	{
		if (fn == null) return null;
		if (typeof to_merge == 'undefined') to_merge = true;
		var file = fn == '-'? new File() : new File(fn);
		var buf = new Bytes();
		var bed = {};
		while (file.readline(buf) >= 0) {
			var t = buf.toString().split("\t");
			if (bed[t[0]] == null) bed[t[0]] = [];
			bed[t[0]].push([parseInt(t[1]), parseInt(t[2])]);
		}
		buf.destroy();
		file.close();

		for (var chr in bed) {
			Interval.sort(bed[chr]);
			if (to_merge)
				Interval.merge(bed[chr], true);
			Interval.index_end(bed[chr], true);
		}
		return bed;
	}

	var re_cigar = /(\d+)([MID])/g, re_tag = /^(\S\S):([AZif]):(\S+)$/;
	var c, to_merge = false, min_mapq = 5, min_len = 50000, max_div = 2.0;
	var re = /(\d+)([MID])/g;
	while ((c = getopt(args, "mq:l:d:")) != null) {
		if (c == 'm') to_merge = true;
		else if (c == 'q') min_mapq = parseInt(getopt.arg);
		else if (c == 'l') min_len = parseInt(getopt.arg);
		else if (c == 'd') max_div = parseFloat(getopt.arg);
	}
	if (args.length - getopt.ind < 2) {
		print("Usage: paftools.js liftover [options] <aln.paf> <query.bed>");
		print("Options:");
		print("  -q INT    min mapping quality [" + min_mapq + "]");
		print("  -l INT    min alignment length [" + min_len + "]");
		print("  -d FLOAT  max sequence divergence (>=1 to disable) [1]");
		exit(1);
	}
	var bed = read_bed(args[getopt.ind+1], to_merge);

	var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
	var buf = new Bytes();
	while (file.readline(buf) >= 0) {
		var t = buf.toString().split("\t");

		if (bed[t[0]] == null) continue; // sequence not present in BED; skip

		// parse tp and cg tags
		var m, tp = null, cg = null;
		for (var i = 12; i < t.length; ++i) {
			if ((m = re_tag.exec(t[i])) != null) {
				if (m[1] == 'tp') tp = m[3];
				else if (m[1] == 'cg') cg = m[3];
			}
		}
		if (tp != 'P' && tp != 'I') continue; // only process primary alignments
		if (cg == null) throw Error("unable to find the 'cg' tag");

		// filter out bad alignments and check overlaps
		for (var i = 1; i <= 3; ++i)
			t[i] = parseInt(t[i]);
		for (var i = 6; i <= 11; ++i)
			t[i] = parseInt(t[i]);
		if (t[11] < min_mapq || t[10] < min_len) continue;
		var regs = Interval.find_ovlp(bed[t[0]], t[2], t[3]);
		if (regs.length == 0) continue; // not overlapping any regions in input BED
		if (max_div >= 0.0 && max_div < 1.0) {
			var n_gaps = 0, n_opens = 0;
			while ((m = re_cigar.exec(cg)) != null)
				if (m[2] == 'I' || m[2] == 'D')
					n_gaps += parseInt(m[1]), ++n_opens;
			var n_mm = t[10] - t[9] - n_gaps;
			var n_diff2 = n_mm + n_opens;
			if (n_diff2 / (n_diff2 + t[9]) > max_div)
				continue;
		}

		// extract start and end positions
		var a = [], r = [], strand = t[4];
		for (var i = 0; i < regs.length; ++i) {
			var s = regs[i][0], e = regs[i][1];
			if (strand == '+') {
				a.push([s, 0, i, -2]);
				a.push([e - 1, 1, i, -2]);
			} else {
				a.push([t[1] - e, 0, i, -2]);
				a.push([t[1] - s - 1, 1, i, -2]);
			}
			r.push([-2, -2]);
		}
		a.sort(function(x, y) { return x[0] - y[0] });

		// lift start/end positions
		var k = 0, x = t[7], y = strand == '+'? t[2] : t[1] - t[3];
		while ((m = re_cigar.exec(cg)) != null) { // TODO: be more careful about edge cases
			var len = parseInt(m[1]);
			if (m[2] == 'D') { // do nothing for D
				x += len;
				continue;
			}
			while (k < a.length && a[k][0] < y) ++k; // skip out-of-range positions
			for (var i = k; i < a.length; ++i) {
				if (y <= a[i][0] && a[i][0] < y + len)
					a[i][3] = m[2] == 'M'? x + (a[i][0] - y) : x;
				else break;
			}
			y += len;
			if (m[2] == 'M') x += len;
		}
		if (x != t[8] || (strand == '+' && y != t[3]) || (strand == '-' && y != t[1] - t[2]))
			throw Error("CIGAR is inconsistent with mapping coordinates");

		// generate result
		for (var i = 0; i < a.length; ++i) {
			if (a[i][1] == 0) r[a[i][2]][0] = a[i][3];
			else r[a[i][2]][1] = a[i][3] + 1; // change to half-close-half-open
		}
		for (var i = 0; i < r.length; ++i) {
			var name = [t[0], regs[i][0], regs[i][1]].join("_");
			if (r[i][0] < 0) name += "_t5", r[i][0] = t[7];
			if (r[i][1] < 0) name += "_t3", r[i][1] = t[8];
			print(t[5], r[i][0], r[i][1], name, 0, strand);
		}
	}
	buf.destroy();
	file.close();
}

// variant calling
function paf_call(args)
{
	var re_cs = /([:=*+-])(\d+|[A-Za-z]+)/g, re_tag = /\t(\S\S:[AZif]):(\S+)/g;
	var c, min_cov_len = 10000, min_var_len = 50000, gap_thres = 50, min_mapq = 5;
	var fa_tmp = null, fa, fa_lens, is_vcf = false;
	while ((c = getopt(args, "l:L:g:q:B:f:")) != null) {
		if (c == 'l') min_cov_len = parseInt(getopt.arg);
		else if (c == 'L') min_var_len = parseInt(getopt.arg);
		else if (c == 'g') gap_thres = parseInt(getopt.arg);
		else if (c == 'q') min_mapq = parseInt(getopt.arg);
		else if (c == 'f') fa_tmp = fasta_read(getopt.arg, fa_lens);
	}
	if (fa_tmp != null) fa = fa_tmp[0], fa_lens = fa_tmp[1], is_vcf = true;

	if (args.length == getopt.ind) {
		print("Usage: sort -k6,6 -k8,8n <with-cs.paf> | paftools.js call [options] -");
		print("Options:");
		print("  -l INT    min alignment length to compute coverage ["+min_cov_len+"]");
		print("  -L INT    min alignment length to call variants ["+min_var_len+"]");
		print("  -q INT    min mapping quality ["+min_mapq+"]");
		print("  -g INT    short/long gap threshold (for statistics only) ["+gap_thres+"]");
		print("  -f FILE   reference sequences (enabling VCF output) [null]");
		exit(1);
	}

	var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
	var buf = new Bytes();
	var tot_len = 0, n_sub = [0, 0, 0], n_ins = [0, 0, 0, 0], n_del = [0, 0, 0, 0];

	function print_vcf(o, fa)
	{
		var v = null;
		if (o[3] != 1) return; // coverage is one; skip
		if (o[5] == '-' && o[6] == '-') return;
		if (o[5] != '-' && o[6] != '-') { // snp
			v = [o[0], o[1] + 1, '.', o[5].toUpperCase(), o[6].toUpperCase()];
		} else if (o[1] > 0) { // shouldn't happen in theory
			if (fa[o[0]] == null) throw Error('sequence "' + o[0] + '" is absent from the reference FASTA');
			if (o[1] >= fa[o[0]].length) throw Error('position ' + o[1] + ' exceeds the length of sequence "' + o[0] + '"');
			var ref = String.fromCharCode(fa[o[0]][o[1]-1]).toUpperCase();
			if (o[5] == '-') // insertion
				v = [o[0], o[1], '.', ref, ref + o[6].toUpperCase()];
			else // deletion
				v = [o[0], o[1], '.', ref + o[5].toUpperCase(), ref];
		}
		v.push(o[4], '.', 'QNAME=' + o[7] + ';QSTART=' + (o[8]+1) + ';QSTRAND=' + (rev? '-' : '+'), 'GT', '1/1');
		if (v == null) throw Error("unexpected variant: [" + o.join(",") + "]");
		print(v.join("\t"));
	}

	function count_var(o)
	{
		if (o[3] > 1) return;
		if (o[5] == '-' && o[6] == '-') return;
		if (o[5] == '-') { // insertion
			var l = o[6].length;
			if (l == 1) ++n_ins[0];
			else if (l == 2) ++n_ins[1];
			else if (l < gap_thres) ++n_ins[2];
			else ++n_ins[3];
		} else if (o[6] == '-') { // deletion
			var l = o[5].length;
			if (l == 1) ++n_del[0];
			else if (l == 2) ++n_del[1];
			else if (l < gap_thres) ++n_del[2];
			else ++n_del[3];
		} else {
			++n_sub[0];
			var s = (o[5] + o[6]).toLowerCase();
			if (s == 'ag' || s == 'ga' || s == 'ct' || s == 'tc')
				++n_sub[1];
			else ++n_sub[2];
		}
	}

	if (is_vcf) {
		print('##fileformat=VCFv4.1');
		for (var i = 0; i < fa_lens.length; ++i)
			print('##contig=<ID=' + fa_lens[i][0] + ',length=' + fa_lens[i][1] + '>');
		print('##INFO=<ID=QNAME,Number=1,Type=String,Description="Query name">');
		print('##INFO=<ID=QSTART,Number=1,Type=Integer,Description="Query start">');
		print('##INFO=<ID=QSTRAND,Number=1,Type=String,Description="Query strand">');
		print('##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">');
		print('#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample');
	}

	var a = [], out = [];
	var c1_ctg = null, c1_start = 0, c1_end = 0, c1_counted = false, c1_len = 0;
	while (file.readline(buf) >= 0) {
		var line = buf.toString();
		var m, t = line.split("\t", 12);
		for (var i = 6; i <= 11; ++i)
			t[i] = parseInt(t[i]);
		if (t[10] < min_cov_len || t[11] < min_mapq) continue;
		//print(t[0], t[7], t[8], c1_start, c1_end);
		for (var i = 1; i <= 3; ++i)
			t[i] = parseInt(t[i]);
		var ctg = t[5], x = t[7], end = t[8];
		var query = t[0], rev = (t[4] == '-'), y = rev? t[3] : t[2];
		// collect tags
		var cs = null, tp = null, have_s1 = false, have_s2 = false;
		while ((m = re_tag.exec(line)) != null) {
			if (m[1] == 'cs:Z') cs = m[2];
			else if (m[1] == 'tp:A') tp = m[2];
			else if (m[1] == 's1:i') have_s1 = true;
			else if (m[1] == 's2:i') have_s2 = true;
		}
		if (have_s1 && !have_s2) continue;
		if (tp != null && (tp == 'S' || tp == 'i')) continue;
		// compute regions covered by 1 contig
		if (ctg != c1_ctg || x >= c1_end) {
			if (c1_counted && c1_end > c1_start) {
				c1_len += c1_end - c1_start;
				if (!is_vcf) print('R', c1_ctg, c1_start, c1_end);
			}
			c1_ctg = ctg, c1_start = x, c1_end = end;
			c1_counted = (t[10] >= min_var_len);
		} else if (end > c1_end) { // overlap
			if (c1_counted && x > c1_start) {
				c1_len += x - c1_start;
				if (!is_vcf) print('R', c1_ctg, c1_start, x);
			}
			c1_start = c1_end, c1_end = end;
			c1_counted = (t[10] >= min_var_len);
		} else if (end > c1_start) { // contained
			if (c1_counted && x > c1_start) {
				c1_len += x - c1_start;
				if (!is_vcf) print('R', c1_ctg, c1_start, x);
			}
			c1_start = end;
		} // else, the alignment precedes the cov1 region; do nothing
		// output variants ahead of this alignment
		while (out.length) {
			if (out[0][0] != ctg || out[0][2] <= x) {
				count_var(out[0]);
				if (is_vcf) print_vcf(out[0], fa);
				else print('V', out[0].join("\t"));
				out.shift();
			} else break;
		}
		// update coverage
		for (var i = 0; i < out.length; ++i)
			if (out[i][1] >= x && out[i][2] <= end)
				++out[i][3];
		// drop alignments that don't overlap with the current one
		var k = 0;
		for (var i = 0; i < a.length; ++i)
			if (a[i][0] == ctg && a[i][2] > x)
				a[k++] = a[i];
		a.length = k;
		// core loop
		if (t[10] >= min_var_len) {
			if (cs == null) continue; // no cs tag
			var blen = 0, n_diff = 0;
			tot_len += t[10];
			while ((m = re_cs.exec(cs)) != null) {
				var cov = 1;
				if (m[1] == '*' || m[1] == '+' || m[1] == '-')
					for (var i = 0; i < a.length; ++i)
						if (a[i][2] > x) ++cov;
				var qs, qe;
				if (m[1] == '=' || m[1] == ':') {
					var l = m[1] == '='? m[2].length : parseInt(m[2]);
					if (rev) y -= l;
					else y += l;
					x += l, blen += l;
				} else if (m[1] == '*') {
					if (rev) qs = y - 1, qe = y, --y;
					else qs = y, qe = y + 1, ++y;
					var br = m[2].charAt(0), bq = m[2].charAt(1);
					if (br != 'n' && bq != 'n') { // don't call a SNP if there is an ambiguous base
						out.push([t[5], x, x+1, cov, t[11], br, bq, query, qs, qe, rev? '-' : '+']);
						++n_diff;
					}
					++x, ++blen;
				} else if (m[1] == '+') {
					var l = m[2].length;
					if (rev) qs = y - l, qe = y, y -= l;
					else qs = y, qe = y + l, y += l;
					out.push([t[5], x, x, cov, t[11], '-', m[2], query, qs, qe, rev? '-' : '+']);
					++blen, ++n_diff;
				} else if (m[1] == '-') {
					var l = m[2].length;
					out.push([t[5], x, x + l, cov, t[11], m[2], '-', query, y, y, rev? '-' : '+']);
					x += l, ++blen, ++n_diff;
				}
			}
		}
		a.push([t[5], t[7], t[8]]);
	}
	if (c1_counted && c1_end > c1_start) {
		c1_len += c1_end - c1_start;
		if (!is_vcf) print('R', c1_ctg, c1_start, c1_end);
	}
	while (out.length) {
		count_var(out[0]);
		if (is_vcf) print_vcf(out[0], fa);
		else print('V', out[0].join("\t"));
		out.shift();
	}

	//warn(tot_len + " alignment columns considered in calling");
	warn(c1_len + " reference bases covered by exactly one contig");
	warn(n_sub[0] + " substitutions; ts/tv = " + (n_sub[1]/n_sub[2]).toFixed(3));
	warn(n_del[0] + " 1bp deletions");
	warn(n_ins[0] + " 1bp insertions");
	warn(n_del[1] + " 2bp deletions");
	warn(n_ins[1] + " 2bp insertions");
	warn(n_del[2] + " [3,"+gap_thres+") deletions");
	warn(n_ins[2] + " [3,"+gap_thres+") insertions");
	warn(n_del[3] + " >="+gap_thres+" deletions");
	warn(n_ins[3] + " >="+gap_thres+" insertions");

	buf.destroy();
	file.close();
	if (fa != null) fasta_free(fa);
}

function paf_stat(args)
{
	var c, gap_out_len = null;
	while ((c = getopt(args, "l:")) != null)
		if (c == 'l') gap_out_len = parseInt(getopt.arg);

	if (getopt.ind == args.length) {
		print("Usage: paftools.js stat [-l gapOutLen] <in.sam>|<in.paf>");
		exit(1);
	}

	var buf = new Bytes();
	var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
	var re = /(\d+)([MIDSHNX=])/g;

	var lineno = 0, n_pri = 0, n_2nd = 0, n_seq = 0, n_cigar_64k = 0, l_tot = 0, l_cov = 0;
	var n_gap = [[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0]];

	function cov_len(regs)
	{
		regs.sort(function(a,b) {return a[0]-b[0]});
		var st = regs[0][0], en = regs[0][1], l = 0;
		for (var i = 1; i < regs.length; ++i) {
			if (regs[i][0] < en)
				en = en > regs[i][1]? en : regs[i][1];
			else l += en - st, st = regs[i][0], en = regs[i][1];
		}
		l += en - st;
		return l;
	}

	var last = null, last_qlen = null, regs = [];
	while (file.readline(buf) >= 0) {
		var line = buf.toString();
		++lineno;
		if (line.charAt(0) != '@') {
			var t = line.split("\t", 12);
			var m, rs, cigar = null, is_pri = false, is_sam = false, is_rev = false, tname = null;
			var atlen = null, aqlen, qs, qe, mapq, ori_qlen;
			if (t[4] == '+' || t[4] == '-') { // PAF
				if (!/\ts2:i:\d+/.test(line)) {
					++n_2nd;
					continue;
				}
				if ((m = /\tcg:Z:(\S+)/.exec(line)) != null)
					cigar = m[1];
				if (cigar == null) {
					warn("WARNING: no CIGAR at line " + lineno);
					continue;
				}
				tname = t[5];
				qs = parseInt(t[2]), qe = parseInt(t[3]);
				aqlen = qe - qs;
				is_rev = t[4] == '+'? false : true;
				rs = parseInt(t[7]);
				atlen = parseInt(t[8]) - rs;
				mapq = parseInt(t[11]);
				ori_qlen = parseInt(t[1]);
			} else { // SAM
				var flag = parseInt(t[1]);
				if ((flag & 4) || t[2] == '*' || t[5] == '*') continue;
				if (flag & 0x100) {
					++n_2nd;
					continue;
				}
				cigar = t[5];
				tname = t[2];
				rs = parseInt(t[3]) - 1;
				mapq = parseInt(t[4]);
				aqlen = t[9].length;
				is_sam = true;
				is_rev = !!(flag&0x10);
			}
			++n_pri;
			if (last != t[0]) {
				if (last != null) {
					l_tot += last_qlen;
					l_cov += cov_len(regs);
				}
				regs = [];
				++n_seq, last = t[0];
			}
			var M = 0, tl = 0, ql = 0, clip = [0, 0], n_cigar = 0, sclip = 0;
			while ((m = re.exec(cigar)) != null) {
				var l = parseInt(m[1]);
				++n_cigar;
				if (m[2] == 'M' || m[2] == '=' || m[2] == 'X') {
					tl += l, ql += l, M += l;
				} else if (m[2] == 'I' || m[2] == 'D') {
					var type;
					if (l < 50) type = 0;
					else if (l < 100) type = 1;
					else if (l < 300) type = 2;
					else if (l < 400) type = 3;
					else if (l < 1000) type = 4;
					else type = 5;
					if (m[2] == 'I') ql += l, ++n_gap[0][type];
					else tl += l, ++n_gap[1][type];
					if (gap_out_len != null && l >= gap_out_len)
						print(t[0], ql, is_rev? '-' : '+', tname, rs + tl, m[2], l);
				} else if (m[2] == 'N') {
					tl += l;
				} else if (m[2] == 'S') {
					clip[M == 0? 0 : 1] = l, sclip += l;
				} else if (m[2] == 'H') {
					clip[M == 0? 0 : 1] = l;
				}
			}
			if (n_cigar > 65535) ++n_cigar_64k;
			if (ql + sclip != aqlen)
				warn("WARNING: aligned query length is inconsistent with CIGAR at line " + lineno + " (" + (ql+sclip) + " != " + aqlen + ")");
			if (atlen != null && atlen != tl)
				warn("WARNING: aligned reference length is inconsistent with CIGAR at line " + lineno);
			if (is_sam) {
				qs = clip[is_rev? 1 : 0], qe = qs + ql;
				ori_qlen = clip[0] + ql + clip[1];
			}
			regs.push([qs, qe]);
			last_qlen = ori_qlen;
		}
	}
	if (regs.length) {
		l_tot += last_qlen;
		l_cov += cov_len(regs);
	}

	file.close();
	buf.destroy();

	if (gap_out_len == null) {
		print("Number of mapped sequences: " + n_seq);
		print("Number of primary alignments: " + n_pri);
		print("Number of secondary alignments: " + n_2nd);
		print("Number of primary alignments with >65535 CIGAR operations: " + n_cigar_64k);
		print("Number of bases in mapped sequences: " + l_tot);
		print("Number of mapped bases: " + l_cov);
		print("Number of insertions in [0,50): " + n_gap[0][0]);
		print("Number of insertions in [50,100): " + n_gap[0][1]);
		print("Number of insertions in [100,300): " + n_gap[0][2]);
		print("Number of insertions in [300,400): " + n_gap[0][3]);
		print("Number of insertions in [400,1000): " + n_gap[0][4]);
		print("Number of insertions in [1000,inf): " + n_gap[0][5]);
		print("Number of deletions in [0,50): " + n_gap[1][0]);
		print("Number of deletions in [50,100): " + n_gap[1][1]);
		print("Number of deletions in [100,300): " + n_gap[1][2]);
		print("Number of deletions in [300,400): " + n_gap[1][3]);
		print("Number of deletions in [400,1000): " + n_gap[1][4]);
		print("Number of deletions in [1000,inf): " + n_gap[1][5]);
	}
}

function paf_bedcov(args)
{
	function read_bed(fn, to_merge, to_dedup)
	{
		var file = new File(fn);
		var buf = new Bytes();
		var h = {};
		while (file.readline(buf) >= 0) {
			var t = buf.toString().split("\t");
			if (h[t[0]] == null)
				h[t[0]] = [];
			var bst = parseInt(t[1]);
			var ben = parseInt(t[2]);
			if (t.length >= 12 && /^\d+$/.test(t[9])) {
				t[9] = parseInt(t[9]);
				var sz = t[10].split(",");
				var st = t[11].split(",");
				for (var i = 0; i < t[9]; ++i) {
					st[i] = parseInt(st[i]);
					sz[i] = parseInt(sz[i]);
					h[t[0]].push([bst + st[i], bst + st[i] + sz[i], 0, 0, 0]);
				}
			} else {
				h[t[0]].push([bst, ben, 0, 0, 0]);
			}
		}
		buf.destroy();
		file.close();
		for (var chr in h) {
			if (to_merge) Interval.merge(h[chr], false);
			else if (to_dedup) Interval.dedup(h[chr], false);
			else Interval.sort(h[chr]);
			Interval.index_end(h[chr]);
		}
		return h;
	}

	var c, print_len = false, to_merge = true, to_dedup = false, fn_excl = null;
	while ((c = getopt(args, "pde:")) != null) {
		if (c == 'p') print_len = true;
		else if (c == 'd') to_dedup = true, to_merge = false;
		else if (c == 'e') fn_excl = getopt.arg;
	}

	if (args.length - getopt.ind < 2) {
		print("Usage: paftools.js bedcov [options] <regions.bed> <target.bed>");
		print("Options:");
		print("  -e FILE    exclude target regions (2nd file) overlapping BED FILE []");
		print("  -p         print number of covered bases for each target");
		exit(1);
	}

	var excl = fn_excl != null? read_bed(fn_excl, true, false) : null;
	var target = read_bed(args[getopt.ind], to_merge, to_dedup);

	var file, buf = new Bytes();
	var tot_len = 0, hit_len = 0;
	file = args[getopt.ind+1] != '-'? new File(args[getopt.ind+1]) : new File();
	while (file.readline(buf) >= 0) {
		var t = buf.toString().split("\t");
		var a = [];
		var bst = parseInt(t[1]);
		var ben = parseInt(t[2]);
		if (t.length >= 12 && /^\d+$/.test(t[9])) { // BED12
			t[9] = parseInt(t[9]);
			var sz = t[10].split(",");
			var st = t[11].split(",");
			for (var i = 0; i < t[9]; ++i) {
				st[i] = parseInt(st[i]);
				sz[i] = parseInt(sz[i]);
				a.push([bst + st[i], bst + st[i] + sz[i], false]);
			}
		} else a.push([bst, ben, false]); // 3-column BED
		var feat_len = 0;
		for (var i = 0; i < a.length; ++i) {
			if (excl != null && excl[t[0]] != null) {
				var oe = Interval.find_ovlp(excl[t[0]], a[i][0], a[i][1]);
				if (oe.length > 0)
					continue;
			}
			a[i][2] = true;
			feat_len += a[i][1] - a[i][0];
		}
		tot_len += feat_len;
		if (target[t[0]] == null) continue;
		var b = [];
		for (var i = 0; i < a.length; ++i) {
			if (!a[i][2]) continue;
			var o = Interval.find_ovlp(target[t[0]], a[i][0], a[i][1]);
			for (var j = 0; j < o.length; ++j) {
				var max_st = o[j][0] > a[i][0]? o[j][0] : a[i][0];
				var min_en = o[j][1] < a[i][1]? o[j][1] : a[i][1];
				b.push([max_st, min_en]);
				o[j][2] += min_en - max_st;
				++o[j][3];
				if (max_st == o[j][0] && min_en == o[j][1])
					++o[j][4];
			}
		}
		// find the length covered
		var feat_hit_len = 0;
		if (b.length > 0) {
			b.sort(function(a,b) {return a[0]-b[0]});
			var st = b[0][0], en = b[0][1];
			for (var i = 1; i < b.length; ++i) {
				if (b[i][0] <= en) en = en > b[i][1]? en : b[i][1];
				else feat_hit_len += en - st, st = b[i][0], en = b[i][1];
			}
			feat_hit_len += en - st;
		}
		hit_len += feat_hit_len;
		if (print_len) print('F', t.slice(0, 4).join("\t"), feat_len, feat_hit_len);
	}
	file.close();

	buf.destroy();

	warn("# target bases: " + tot_len);
	warn("# target bases overlapping regions: " + hit_len + ' (' + (100.0 * hit_len / tot_len).toFixed(2) + '%)');
}

/**********************
 * Conversion related *
 **********************/

function paf_view(args)
{
	var c, line_len = 80, fmt = "aln";
	while ((c = getopt(args, "f:l:")) != null) {
		if (c == 'f') {
			fmt = getopt.arg;
			if (fmt != "aln" && fmt != "lastz-cigar" && fmt != "maf")
				throw Error("format must be one of aln, lastz-cigar and maf");
		} else if (c == 'l') line_len = parseInt(getopt.arg);
	}
	if (line_len == 0) line_len = 0x7fffffff;

	if (getopt.ind == args.length) {
		print("Usage: paftools.js view [options] <in.paf>");
		print("Options:");
		print("  -f STR    output format: aln (BLAST-like), maf or lastz-cigar [aln]");
		print("  -l INT    line length in BLAST-like output [80]");
		exit(1);
	}

	function padding_str(x, len, right)
	{
		var s = x.toString();
		if (s.length < len) {
			if (right) s += Array(len - s.length + 1).join(" ");
			else s = Array(len - s.length + 1).join(" ") + s;
		}
		return s;
	}

	function update_aln(s_ref, s_qry, s_mid, type, seq, slen)
	{
		var l = type == '*'? 1 : seq.length;
		if (type == '=' || type == ':') {
			s_ref.set(seq);
			s_qry.set(seq);
			s_mid.set(Array(l+1).join("|"));
			slen[0] += l, slen[1] += l;
		} else if (type == '*') {
			s_ref.set(seq.charAt(0));
			s_qry.set(seq.charAt(1));
			s_mid.set(' ');
			slen[0] += 1, slen[1] += 1;
		} else if (type == '+') {
			s_ref.set(Array(l+1).join("-"));
			s_qry.set(seq);
			s_mid.set(Array(l+1).join(" "));
			slen[1] += l;
		} else if (type == '-') {
			s_ref.set(seq);
			s_qry.set(Array(l+1).join("-"));
			s_mid.set(Array(l+1).join(" "));
			slen[0] += l;
		}
	}

	function print_aln(rs, qs, strand, slen, elen, s_ref, s_qry, s_mid)
	{
		print(["Ref+:", padding_str(rs + slen[0] + 1, 10, false), s_ref.toString(), padding_str(rs + elen[0], 10, true)].join(" "));
		print("                 " + s_mid.toString());
		var st, en;
		if (strand == '+') st = qs + slen[1] + 1, en = qs + elen[1];
		else st = qs - slen[1], en = qs - elen[1] + 1;
		print(["Qry" + strand + ":", padding_str(st, 10, false), s_qry.toString(), padding_str(en, 10, true)].join(" "));
	}

	var s_ref = new Bytes(), s_qry = new Bytes(), s_mid = new Bytes(); // these are used to show padded alignment
	var re_cs = /([:=\-\+\*])(\d+|[A-Za-z]+)/g;
	var re_cg = /(\d+)([MIDNSH])/g;

	var buf = new Bytes();
	var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
	var lineno = 0;
	if (fmt == "maf") print("##maf version=1\n");
	while (file.readline(buf) >= 0) {
		var m, line = buf.toString();
		var t = line.split("\t", 12);
		++lineno;
		s_ref.length = s_qry.length = s_mid.length = 0;
		var slen = [0, 0], elen = [0, 0];
		if (fmt == "lastz-cigar") { // LASTZ-cigar output
			var cg = (m = /\tcg:Z:(\S+)/.exec(line)) != null? m[1] : null;
			if (cg == null) {
				warn("WARNING: converting to LASTZ-cigar format requires the 'cg' tag, which is absent on line " + lineno);
				continue;
			}
			var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? m[1] : 0;
			var out = ['cigar:', t[0], t[2], t[3], t[4], t[5], t[7], t[8], '+', score];
			while ((m = re_cg.exec(cg)) != null)
				out.push(m[2], m[1]);
			print(out.join(" "));
		} else if (fmt == "maf") { // MAF output
			var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
			if (cs == null) {
				warn("WARNING: converting to MAF requires the 'cs' tag, which is absent on line " + lineno);
				continue;
			}
			while ((m = re_cs.exec(cs)) != null) {
				if (m[1] == ':')
					throw Error("converting to MAF only works with 'minimap2 --cs=long'");
				update_aln(s_ref, s_qry, s_mid, m[1], m[2], elen);
			}
			var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
			var len = t[0].length > t[5].length? t[0].length : t[5].length;
			print("a " + score);
			print(["s", padding_str(t[5], len, true), padding_str(t[7], 10, false), padding_str(parseInt(t[8]) - parseInt(t[7]), 10, false),
					"+", padding_str(t[6], 10, false), s_ref.toString()].join(" "));
			var qs, qe, ql = parseInt(t[1]);
			if (t[4] == '+') {
				qs = parseInt(t[2]);
				qe = parseInt(t[3]);
			} else {
				qs = ql - parseInt(t[3]);
				qe = ql - parseInt(t[2]);
			}
			print(["s", padding_str(t[0], len, true), padding_str(qs, 10, false), padding_str(qe - qs, 10, false),
					t[4], padding_str(ql, 10, false), s_qry.toString()].join(" "));
			print("");
		} else { // BLAST-like output
			var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
			if (cs == null) {
				warn("WARNING: converting to BLAST-like alignment requires the 'cs' tag, which is absent on line " + lineno);
				continue;
			}
			line = line.replace(/\tc[sg]:Z:\S+/g, ""); // get rid of cs or cg tags
			print('>' + line);
			var rs = parseInt(t[7]), qs = t[4] == '+'? parseInt(t[2]) : parseInt(t[3]);
			var n_blocks = 0;
			while ((m = re_cs.exec(cs)) != null) {
				if (m[1] == ':') m[2] = Array(parseInt(m[2]) + 1).join("=");
				var start = 0, rest = m[1] == '*'? 1 : m[2].length;
				while (rest > 0) {
					var l_proc;
					if (s_ref.length + rest >= line_len) {
						l_proc = line_len - s_ref.length;
						update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
						if (n_blocks > 0) print("");
						print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
						++n_blocks;
						s_ref.length = s_qry.length = s_mid.length = 0;
						slen[0] = elen[0], slen[1] = elen[1];
					} else {
						l_proc = rest;
						update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
					}
					rest -= l_proc, start += l_proc;
				}
			}
			if (s_ref.length > 0) {
				if (n_blocks > 0) print("");
				print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
				++n_blocks;
			}
			print("//");
		}
	}
	file.close();
	buf.destroy();

	s_ref.destroy(); s_qry.destroy(); s_mid.destroy();
}

function paf_gff2bed(args)
{
	var c, fn_ucsc_fai = null, is_short = false, keep_gff = false;
	while ((c = getopt(args, "u:sg")) != null) {
		if (c == 'u') fn_ucsc_fai = getopt.arg;
		else if (c == 's') is_short = true;
		else if (c == 'g') keep_gff = true;
	}

	if (getopt.ind == args.length) {
		print("Usage: paftools.js gff2bed [-g] [-u ucsc-genome.fa.fai] <in.gff>");
		exit(1);
	}

	var ens2ucsc = {};
	if (fn_ucsc_fai != null) {
		var buf = new Bytes();
		var file = new File(fn_ucsc_fai);
		while (file.readline(buf) >= 0) {
			var t = buf.toString().split("\t");
			var s = t[0];
			if (/_(random|alt|decoy)$/.test(s)) {
				s = s.replace(/_(random|alt|decoy)$/, '');
				s = s.replace(/^chr\S+_/, '');
			} else {
				s = s.replace(/^chrUn_/, '');
			}
			s = s.replace(/v(\d+)/, ".$1");
			if (s != t[0]) ens2ucsc[s] = t[0];
		}
		file.close();
		buf.destroy();
	}

	var colors = {
		'protein_coding':'0,128,255',
		'lincRNA':'0,192,0',
		'snRNA':'0,192,0',
		'miRNA':'0,192,0',
		'misc_RNA':'0,192,0'
	};

	function print_bed12(exons, cds_st, cds_en, is_short)
	{
		if (exons.length == 0) return;
		var name = is_short? exons[0][7] + "|" + exons[0][5] : exons[0].slice(4, 7).join("|");
		var a = exons.sort(function(a,b) {return a[1]-b[1]});
		var sizes = [], starts = [], st, en;
		st = a[0][1];
		en = a[a.length - 1][2];
		if (cds_st == 1<<30) cds_st = st;
		if (cds_en == 0) cds_en = en;
		if (cds_st < st || cds_en > en)
			throw Error("inconsistent thick start or end for transcript " + a[0][4]);
		for (var i = 0; i < a.length; ++i) {
			sizes.push(a[i][2] - a[i][1]);
			starts.push(a[i][1] - st);
		}
		var color = colors[a[0][5]];
		if (color == null) color = '196,196,196';
		print(a[0][0], st, en, name, 1000, a[0][3], cds_st, cds_en, color, a.length, sizes.join(",") + ",", starts.join(",") + ",");
	}

	var re_gtf = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name) "([^"]+)";/g;
	var re_gff3 = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name)=([^;]+)/g;
	var buf = new Bytes();
	var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);

	var exons = [], cds_st = 1<<30, cds_en = 0, last_id = null;
	while (file.readline(buf) >= 0) {
		var t = buf.toString().split("\t");
		if (keep_gff) {
			if (t[0].charAt(0) != '#' && ens2ucsc[t[0]] != null)
				t[0] = ens2ucsc[t[0]];
			print(t.join("\t"));
			continue;
		}
		if (t[0].charAt(0) == '#') continue;
		if (t[2] != "CDS" && t[2] != "exon") continue;
		t[3] = parseInt(t[3]) - 1;
		t[4] = parseInt(t[4]);
		var id = null, type = "", gname = "N/A", biotype = "", m, tname = "N/A";
		while ((m = re_gtf.exec(t[8])) != null) {
			if (m[1] == "transcript_id") id = m[2];
			else if (m[1] == "transcript_type") type = m[2];
			else if (m[1] == "transcript_biotype") biotype = m[2];
			else if (m[1] == "gene_name") name = m[2];
			else if (m[1] == "transcript_name") tname = m[2];
		}
		while ((m = re_gff3.exec(t[8])) != null) {
			if (m[1] == "transcript_id") id = m[2];
			else if (m[1] == "transcript_type") type = m[2];
			else if (m[1] == "transcript_biotype") biotype = m[2];
			else if (m[1] == "gene_name") name = m[2];
			else if (m[1] == "transcript_name") tname = m[2];
		}
		if (type == "" && biotype != "") type = biotype;
		if (id == null) throw Error("No transcript_id");
		if (id != last_id) {
			print_bed12(exons, cds_st, cds_en, is_short);
			exons = [], cds_st = 1<<30, cds_en = 0;
			last_id = id;
		}
		if (t[2] == "CDS") {
			cds_st = cds_st < t[3]? cds_st : t[3];
			cds_en = cds_en > t[4]? cds_en : t[4];
		} else if (t[2] == "exon") {
			if (fn_ucsc_fai != null) {
				if (ens2ucsc[t[0]] != null)
					t[0] = ens2ucsc[t[0]];
				else if (/^[A-Z]+\d+\.\d+$/.test(t[0]))
					t[0] = t[0].replace(/([A-Z]+\d+)\.(\d+)/, "chrUn_$1v$2");
			}
			exons.push([t[0], t[3], t[4], t[6], id, type, name, tname]);
		}
	}
	if (last_id != null)
		print_bed12(exons, cds_st, cds_en, is_short);

	file.close();
	buf.destroy();
}

function paf_sam2paf(args)
{
	var c, pri_only = false, use_eq = false;
	while ((c = getopt(args, "p")) != null)
		if (c == 'p') pri_only = true;
	if (args.length == getopt.ind) {
		print("Usage: paftools.js sam2paf [-p] <in.sam>");
		exit(1);
	}

	var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
	var buf = new Bytes();
	var re = /(\d+)([MIDSHNX=])/g, re_MD = /(\d+)|(\^[A-Za-z]+)|([A-Za-z])/g, re_tag = /\t(\S\S:[AZif]):(\S+)/g;

	var ctg_len = {}, lineno = 0;
	while (file.readline(buf) >= 0) {
		var m, n_cigar = 0, line = buf.toString();
		++lineno;
		if (line.charAt(0) == '@') {
			if (/^@SQ/.test(line)) {
				var name = (m = /\tSN:(\S+)/.exec(line)) != null? m[1] : null;
				var l = (m = /\tLN:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
				if (name != null && l != null) ctg_len[name] = l;
			}
			continue;
		}
		var t = line.split("\t", 11);
		var flag = parseInt(t[1]);
		if (t[9] != '*' && t[10] != '*' && t[9].length != t[10].length)
			throw Error("at line " + lineno + ": inconsistent SEQ and QUAL lengths - " + t[9].length + " != " + t[10].length);
		if (t[2] == '*' || (flag&4) || t[5] == '*') continue;
		if (pri_only && (flag&0x100)) continue;
		var tlen = ctg_len[t[2]];
		if (tlen == null) throw Error("at line " + lineno + ": can't find the length of contig " + t[2]);
		// find tags
		var nn = 0, NM = null, MD = null, md_list = [];
		while ((m = re_tag.exec(line)) != null) {
			if (m[1] == "NM:i") NM = parseInt(m[2]);
			else if (m[1] == "nn:i") nn = parseInt(m[2]);
			else if (m[1] == "MD:Z") MD = m[2];
		}
		if (t[9] == '*') MD = null;
		// infer various lengths from CIGAR
		var clip = [0, 0], soft_clip = 0, I = [0, 0], D = [0, 0], M = 0, N = 0, mm = 0, have_M = false, have_ext = false, cigar = [];
		while ((m = re.exec(t[5])) != null) {
			var l = parseInt(m[1]), op = m[2];
			if (op == 'M') M += l, have_M = true;
			else if (op == 'I') ++I[0], I[1] += l;
			else if (op == 'D') ++D[0], D[1] += l;
			else if (op == 'N') N += l;
			else if (op == 'S') clip[n_cigar == 0? 0 : 1] = l, soft_clip += l;
			else if (op == 'H') clip[n_cigar == 0? 0 : 1] = l;
			else if (op == '=') M += l, have_ext = true, op = 'M';
			else if (op == 'X') M += l, mm += l, have_ext = true, op = 'M';
			++n_cigar;
			if (MD != null && op != 'H') {
				if (cigar.length > 0 && cigar[cigar.length-1][1] == op)
					cigar[cigar.length-1][0] += l;
				else cigar.push([l, op]);
			}
		}
		var ql = M + I[1] + soft_clip;
		var tl = M + D[1] + N;
		var ts = parseInt(t[3]) - 1, te = ts + tl;
		// checking coordinate and length consistencies
		if (n_cigar > 65535)
			warn("WARNING at line " + lineno + ": " + n_cigar + " CIGAR operations");
		if (te > tlen) {
			warn("WARNING at line " + lineno + ": alignment end position larger than ref length; skipped");
			continue;
		}
		if (t[9] != '*' && t[9].length != ql) {
			warn("WARNING at line " + lineno + ": SEQ length inconsistent with CIGAR (" + t[9].length + " != " + ql + "); skipped");
			continue;
		}
		// parse MD
		var cs = [];
		if (MD != null) {
			var k = 0, cx = 0, cy = 0, mx = 0, my = 0;
			while ((m = re_MD.exec(MD)) != null) {
				if (m[2] != null) { // deletion from the reference
					var len = m[2].length - 1;
					cs.push('-', m[2].substr(1));
					mx += len, cx += len, ++k;
				} else { // copy or mismatch
					var ml = m[1] != null? parseInt(m[1]) : 1;
					while (k < cigar.length && cigar[k][1] != 'D') {
						var cl = cigar[k][0], op = cigar[k][1];
						if (op == 'M') {
							if (my + ml < cy + cl) {
								if (ml > 0) {
									if (m[3] != null) cs.push('*', m[3], t[9][my]);
									else cs.push(':', ml);
								}
								mx += ml, my += ml, ml = 0;
								break;
							} else {
								var dl = cy + cl - my;
								cs.push(':', dl);
								cx += cl, cy += cl, ++k;
								mx += dl, my += dl, ml -= dl;
							}
						} else if (op == 'I') {
							cs.push('+', t[9].substr(cy, cl));
							cy += cl, my += cl, ++k;
						} else if (op == 'S') {
							cy += cl, my += cl, ++k;
						} else throw Error("at line " + lineno + ": inconsistent MD tag");
					}
					if (ml != 0) throw Error("at line " + lineno + ": inconsistent MD tag");
				}
			}
			if (cx != mx || cy != my) throw Error("at line " + lineno + ": inconsistent MD tag");
		}
		// compute matching length, block length and calibrate NM
		if (have_ext && !have_M) { // extended CIGAR
			if (NM != null && NM != I[1] + D[1] + mm)
				warn("WARNING at line " + lineno + ": NM is different from sum of gaps and mismatches");
			NM = I[1] + D[1] + mm;
		} else if (NM != null) { // standard CIGAR; NM present
			if (NM < I[1] + D[1]) {
				warn("WARNING at line " + lineno + ": NM is less than the total number of gaps (" + NM + " < " + (I[1]+D[1]) + ")");
				NM = I[1] + D[1];
			}
			mm = NM - (I[1] + D[1]);
		} else { // no way to compute mm
			warn("WARNING at line " + lineno + ": unable to find the number of mismatches; assuming zero");
			mm = 0;
		}
		var mlen = M - mm;
		var blen = M + I[1] + D[1];
		// find query name, start and end
		var qlen = M + I[1] + clip[0] + clip[1];
		var qname = t[0], qs, qe;
		if ((flag&1) && (flag&0x40)) qname += '/1';
		if ((flag&1) && (flag&0x80)) qname += '/2';
		if (flag&16) qs = clip[1], qe = qlen - clip[0];
		else qs = clip[0], qe = qlen - clip[1];
		// optional tags
		var type = flag&0x100? 'S' : 'P';
		var tags = ["tp:A:" + type];
		if (NM != null) tags.push("mm:i:"+mm);
		tags.push("gn:i:"+(I[1]+D[1]), "go:i:"+(I[0]+D[0]), "cg:Z:" + t[5].replace(/\d+[SH]/g, ''));
		if (cs.length > 0) tags.push("cs:Z:" + cs.join(""));
		// print out
		var a = [qname, qlen, qs, qe, flag&16? '-' : '+', t[2], tlen, ts, te, mlen, blen, t[4]];
		print(a.join("\t"), tags.join("\t"));
	}

	buf.destroy();
	file.close();
}

function paf_delta2paf(args)
{
	if (args.length == 0) {
		print("Usage: paftools.js delta2paf <in.delta>");
		exit(1);
	}

	var buf = new Bytes();
	var file = args[0] == '-'? new File() : new File(args[0]);

	var rname, qname, rlen, qlen, qs, qe, rs, re, strand, NM, cigar, x, y, seen_gt = false;
	while (file.readline(buf) >= 0) {
		var m, line = buf.toString();
		if ((m = /^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/.exec(line)) != null) {
			rname = m[1], qname = m[2], rlen = parseInt(m[3]), qlen = parseInt(m[4]);
			seen_gt = true;
			continue;
		}
		if (!seen_gt) continue;
		var t = line.split(" ");
		if (t.length == 7) {
			for (var i = 0; i < 5; ++i)
				t[i] = parseInt(t[i]);
			strand = ((t[0] < t[1] && t[2] < t[3]) || (t[0] > t[1] && t[2] > t[3]))? 1 : -1;
			rs = (t[0] < t[1]? t[0] : t[1]) - 1;
			re = t[1] > t[0]? t[1] : t[0];
			qs = (t[2] < t[3]? t[2] : t[3]) - 1;
			qe = t[3] > t[2]? t[3] : t[2];
			x = y = 0;
			NM = parseInt(t[4]);
			cigar = [];
		} else if (t.length == 1) {
			var d = parseInt(t[0]);
			if (d == 0) {
				var blen = 0, cigar_str = [];
				if (re - rs - x != qe - qs - y) throw Error("inconsisnt alignment");
				cigar.push((re - rs - x) << 4);
				for (var i = 0; i < cigar.length; ++i) {
					blen += cigar[i] >> 4;
					cigar_str.push((cigar[i]>>4) + "MID".charAt(cigar[i]&0xf));
				}
				print([qname, qlen, qs, qe, strand > 0? '+' : '-', rname, rlen, rs, re, blen - NM, blen, 0, "NM:i:" + NM, "cg:Z:" + cigar_str.join("")].join("\t"));
			} else if (d > 0) {
				var l = d - 1;
				x += l + 1, y += l;
				if (l > 0) cigar.push(l<<4);
				if (cigar.length > 0 && (cigar[cigar.length-1]&0xf) == 2)
					cigar[cigar.length-1] += 1<<4;
				else cigar.push(1<<4|2); // deletion
			} else {
				var l = -d - 1;
				x += l, y += l + 1;
				if (l > 0) cigar.push(l<<4);
				if (cigar.length > 0 && (cigar[cigar.length-1]&0xf) == 1)
					cigar[cigar.length-1] += 1<<4;
				else cigar.push(1<<4|1); // insertion
			}
		}
	}
	file.close();
	buf.destroy();
}

function paf_splice2bed(args)
{
	var colors = ["0,128,255", "255,0,0", "0,192,0"];

	function print_lines(a, fmt, keep_multi)
	{
		if (a.length == 0) return;
		if (fmt == "bed") {
			var n_pri = 0;
			for (var i = 0; i < a.length; ++i)
				if (a[i][8] == 0) ++n_pri;
			if (n_pri > 1) {
				for (var i = 0; i < a.length; ++i)
					if (a[i][8] == 0) a[i][8] = 1;
			} else if (n_pri == 0) {
				warn("Warning: " + a[0][3] + " doesn't have a primary alignment");
			}
			for (var i = 0; i < a.length; ++i) {
				if (!keep_multi && a[i][8] == 2) continue;
				a[i][8] = colors[a[i][8]];
				print(a[i].join("\t"));
			}
		}
		a.length = 0;
	}

	var re = /(\d+)([MIDNSH])/g;
	var c, fmt = "bed", fn_name_conv = null, keep_multi = false;
	while ((c = getopt(args, "f:n:m")) != null) {
		if (c == 'f') fmt = getopt.arg;
		else if (c == 'n') fn_name_conv = getopt.arg;
		else if (c == 'm') keep_multi = true;
	}
	if (getopt.ind == args.length) {
		print("Usage: paftools.js splice2bed [options] <in.paf>|<in.sam>");
		print("Options:");
		print("  -m      keep multiple mappings (SAM flag 0x100)");
		exit(1);
	}

	var conv = null;
	if (fn_name_conv != null) {
		conv = new Map();
		var file = new File(fn_name_conv);
		var buf = new Bytes();
		while (file.readline(buf) >= 0) {
			var t = buf.toString().split("\t");
			conv.put(t[0], t[1]);
		}
		buf.destroy();
		file.close();
	}

	var file = args[getopt.ind] == '-'? new 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");
		var is_pri = false, cigar = null, a1;
		var qname = conv != null? conv.get(t[0]) : null;
		if (qname != null) t[0] = qname;
		if (t.length >= 10 && t[4] != '+' && t[4] != '-' && /^\d+/.test(t[1])) { // SAM
			var flag = parseInt(t[1]);
			if (flag&1) t[0] += '/' + (flag>>6&3);
		}
		if (a.length && a[0][3] != t[0]) {
			print_lines(a, fmt, keep_multi);
			a = [];
		}
		if (t.length >= 12 && (t[4] == '+' || t[4] == '-')) { // PAF
			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;
				}
			}
			a1 = [t[5], t[7], t[8], t[0], Math.floor(t[9]/t[10]*1000), t[4]];
		} else if (t.length >= 10) { // SAM
			var flag = parseInt(t[1]);
			if ((flag&4) || a[2] == '*') continue;
			cigar = t[5];
			is_pri = (flag&0x100)? false : true;
			a1 = [t[2], parseInt(t[3])-1, null, t[0], 1000, (flag&16)? '-' : '+'];
		} else {
			throw Error("unrecognized input format");
		}
		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);
		// write the BED12 line
		if (a1[2] == null) a1[2] = a1[1] + x;
		a1.push(a1[1], a1[2]); // thick start/end is the same as start/end
		a1.push(is_pri? 0 : 2, bs.length, bl.join(",")+",", bs.join(",")+",");
		a.push(a1);
	}
	print_lines(a, fmt, keep_multi);
	buf.destroy();
	file.close();
	if (conv != null) conv.destroy();
}

/**********************
 * Evaluation related *
 **********************/

// evaluate mapping accuracy
function paf_mapeval(args)
{
	var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.1, cap_short_mapq = false;
	while ((c = getopt(args, "Q:r:m:c")) != null) {
		if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true;
		else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg);
		else if (c == 'm') mode = parseInt(getopt.arg);
		else if (c == 'c') cap_short_mapq = true;
	}

	if (args.length == getopt.ind) {
		warn("Usage: paftools.js mapeval [options] <in.paf>|<in.sam>");
		warn("Options:");
		warn("  -r FLOAT   mapping correct if overlap_length/union_length>FLOAT [" + ovlp_ratio + "]");
		warn("  -Q INT     print wrong mappings with mapQ>INT [don't print]");
		warn("  -m INT     0: eval the longest aln only; 1: first aln only; 2: all primary aln [0]");
		exit(1);
	}

	var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
	var buf = new Bytes();

	var tot = [], err = [];
	for (var q = 0; q <= max_mapq; ++q)
		tot[q] = err[q] = 0;

	function is_correct(s, b)
	{
		if (s[0] != b[0] || s[3] != b[3]) return false;
		var o, l;
		if (s[1] < b[1]) {
			if (s[2] <= b[1]) return false;
			o = (s[2] < b[2]? s[2] : b[2]) - b[1];
			l = (s[2] > b[2]? s[2] : b[2]) - s[1];
		} else {
			if (b[2] <= s[1]) return false;
			o = (s[2] < b[2]? s[2] : b[2]) - s[1];
			l = (s[2] > b[2]? s[2] : b[2]) - b[1];
		}
		return o/l > ovlp_ratio? true : false;
	}

	function count_err(qname, a, tot, err, mode)
	{
		if (a.length == 0) return;

		var m, s;
		if ((m = /^(\S+)!(\S+)!(\d+)!(\d+)!([\+\-])$/.exec(qname)) != null) { // pbsim single-end reads
			s = [m[1], m[2], parseInt(m[3]), parseInt(m[4]), m[5]];
		} else if ((m = /^(\S+)!(\S+)!(\d+)_(\d+)!(\d+)_(\d+)!([\+\-])([\+\-])\/([12])$/.exec(qname)) != null) { // mason2 paired-end reads
			if (m[9] == '1') {
				s = [m[1], m[2], parseInt(m[3]), parseInt(m[5]), m[7]];
			} else {
				s = [m[1], m[2], parseInt(m[4]), parseInt(m[6]), m[8]];
			}
		} else throw Error("Failed to parse simulated read names '" + qname + "'");
		s.shift(); // skip the orginal read name

		if (mode == 0 || mode == 1) { // longest only or first only
			var max_i = 0;
			if (mode == 0) { // longest only
				var max = 0;
				for (var i = 0; i < a.length; ++i)
					if (a[i][5] > max)
						max = a[i][5], max_i = i;
			}
			var mapq = a[max_i][4];
			++tot[mapq];
			if (!is_correct(s, a[max_i])) {
				if (mapq >= err_out_q)
					print('E', qname, a[max_i].join("\t"));
				++err[mapq];
			}
		} else if (mode == 2) { // all primary mode
			var max_err_mapq = -1, max_mapq = 0, max_err_i = -1;
			if (cap_short_mapq) {
				var max = 0, max_q = 0;
				for (var i = 0; i < a.length; ++i)
					if (a[i][5] > max)
						max = a[i][5], max_q = a[i][4];
				for (var i = 0; i < a.length; ++i)
					a[i][4] = max_q < a[i][4]? max_q : a[i][4];
			}
			for (var i = 0; i < a.length; ++i) {
				max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4];
				if (!is_correct(s, a[i]))
					if (a[i][4] > max_err_mapq)
						max_err_mapq = a[i][4], max_err_i = i;
			}
			if (max_err_mapq >= 0) {
				++tot[max_err_mapq], ++err[max_err_mapq];
				if (max_err_mapq >= err_out_q)
					print('E', qname, a[max_err_i].join("\t"));
			} else ++tot[max_mapq];
		}
	}

	var lineno = 0, last = null, a = [], n_unmapped = null;
	var re_cigar = /(\d+)([MIDSHN])/g;
	while (file.readline(buf) >= 0) {
		var m, line = buf.toString();
		++lineno;
		if (line[0] != '@') {
			var t = line.split("\t");
			if (t[4] == '+' || t[4] == '-') { // PAF
				if (last != t[0]) {
					if (last != null) count_err(last, a, tot, err, mode);
					a = [], last = t[0];
				}
				if (/\ts1:i:\d+/.test(line) && !/\ts2:i:\d+/.test(line)) // secondary alignment in minimap2 PAF
					continue;
				var mapq = parseInt(t[11]);
				if (mapq > max_mapq) mapq = max_mapq;
				a.push([t[5], parseInt(t[7]), parseInt(t[8]), t[4], mapq, parseInt(t[9])]);
			} else { // SAM
				var flag = parseInt(t[1]);
				var read_no = flag>>6&0x3;
				var qname = t[0];
				if (!/\/[12]$/.test(qname))
					qname = read_no == 1 || read_no == 2? t[0] + '/' + read_no : t[0];
				if (last != qname) {
					if (last != null) count_err(last, a, tot, err, mode);
					a = [], last = qname;
				}
				if (flag&0x100) continue; // secondary alignment
				if ((flag&0x4) || t[2] == '*') { // unmapped
					if (n_unmapped == null) n_unmapped = 0;
					++n_unmapped;
					continue;
				}
				var mapq = parseInt(t[4]);
				if (mapq > max_mapq) mapq = max_mapq;
				var pos = parseInt(t[3]) - 1, pos_end = pos;
				var n_gap = 0, mlen = 0;
				while ((m = re_cigar.exec(t[5])) != null) {
					var len = parseInt(m[1]);
					if (m[2] == 'M') pos_end += len, mlen += len;
					else if (m[2] == 'I') n_gap += len;
					else if (m[2] == 'D') n_gap += len, pos_end += len;
				}
				var score = pos_end - pos;
				if ((m = /\tNM:i:(\d+)/.exec(line)) != null) {
					var NM = parseInt(m[1]);
					if (NM >= n_gap) score = mlen - (NM - n_gap);
				}
				a.push([t[2], pos, pos_end, (flag&16)? '-' : '+', mapq, score]);
			}
		}
	}
	if (last != null) count_err(last, a, tot, err, mode);

	buf.destroy();
	file.close();

	var sum_tot = 0, sum_err = 0, q_out = -1, sum_tot2 = 0, sum_err2 = 0;
	for (var q = max_mapq; q >= 0; --q) {
		if (tot[q] == 0) continue;
		if (q_out < 0 || err[q] > 0) {
			if (q_out >= 0) print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9), sum_tot2);
			sum_tot = sum_err = 0, q_out = q;
		}
		sum_tot += tot[q], sum_err += err[q];
		sum_tot2 += tot[q], sum_err2 += err[q];
	}
	print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9), sum_tot2);
	if (n_unmapped != null) print('U', n_unmapped);
}

// convert mason2 SAM to FASTQ
function paf_mason2fq(args)
{
	if (args.length == 0) {
		print("Usage: paftools.js mason2fq <mason.sam>");
		exit(1);
	}

	function print_se(a)
	{
		print('@' + a.slice(0, 5).join("!") + " " + a[8]);
		print(a[5]);
		print("+");
		print(a[6]);
	}

	var buf = new Bytes(), buf2 = new Bytes();
	var file = new File(args[0]);
	var re = /(\d+)([MIDSHN])/g;
	var last = null;
	while (file.readline(buf) >= 0) {
		var t = buf.toString().split("\t");
		if (t[0].charAt(0) == '@') continue;
		var m, l_ref = 0;
		while ((m = re.exec(t[5])) != null)
			if (m[2] == 'D' || m[2] == 'M' || m[2] == 'N')
				l_ref += parseInt(m[1]);
		var flag = parseInt(t[1]);
		var rev = !!(flag&16);
		var seq, qual;
		if (rev) {
			buf2.length = 0;
			buf2.set(t[9], 0);
			buf2.revcomp();
			seq = buf2.toString();
			buf2.set(t[10], 0);
			buf2.reverse();
			qual = buf2.toString();
		} else seq = t[9], qual = t[10];
		var qname = t[0];
		qname = qname.replace(/^simulated./, "");
		var chr = t[2];
		var pos = parseInt(t[3]) - 1;
		var strand = (flag&16)? '-' : '+';
		var read_no = flag&0xc0;
		if (read_no == 0x40) read_no = 1;
		else if (read_no == 0x80) read_no = 2;
		else read_no = 0;
		var err = 0, snp = 0, indel = 0;
		for (var i = 11; i < t.length; ++i) {
			if ((m = /^XE:i:(\d+)/.exec(t[i])) != null) err = m[1];
			else if ((m = /^XS:i:(\d+)/.exec(t[i])) != null) snp = m[1];
			else if ((m = /^XI:i:(\d+)/.exec(t[i])) != null) indel = m[1];
		}
		var comment = [err, snp, indel].join(":");
		if (last == null) {
			last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
		} else if (last[0] != qname) {
			print_se(last);
			last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
		} else {
			if (read_no == 2) { // last[] is the first read
				if (last[7] != 1) throw Error("ERROR: can't find read1");
				var name = [qname, chr, last[2] + "_" + pos, last[3] + "_" + (pos + l_ref), last[4] + strand].join("!");
				print('@' + name + '/1' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
				print('@' + name + '/2' + ' ' + comment); print(seq); print("+"); print(qual);
			} else {
				if (last[7] != 2) throw Error("ERROR: can't find read2");
				var name = [qname, chr, pos + "_" + last[2], (pos + l_ref) + "_" + last[3], strand + last[4]].join("!");
				print('@' + name + '/1' + ' ' + comment); print(seq); print("+"); print(qual);
				print('@' + name + '/2' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
			}
			last = null;
		}
	}
	if (last != null) print_se(last);
	file.close();
	buf.destroy();
	buf2.destroy();
}

// convert pbsim MAF to FASTQ
function paf_pbsim2fq(args)
{
	if (args.length < 2) {
		print("Usage: paftools.js pbsim2fq <ref.fa.fai> <pbsim1.maf> [[pbsim2.maf] ...]");
		exit(1);
	}

	var file, buf = new Bytes(), buf2 = new Bytes();
	file = new File(args[0]);
	var chr_list = [];
	while (file.readline(buf) >= 0) {
		var t = buf.toString().split(/\s+/);
		chr_list.push(t[0]);
	}
	file.close();

	for (var k = 1; k < args.length; ++k) {
		var fn = args[k];
		file = new File(fn);
		var state = 0, reg;
		while (file.readline(buf) >= 0) {
			var line = buf.toString();
			if (state == 0 && line.charAt(0) == 'a') {
				state = 1;
			} else if (state == 1 && line.charAt(0) == 's') {
				var t = line.split(/\s+/);
				var st = parseInt(t[2]);
				reg = [st, st + parseInt(t[3])];
				state = 2;
			} else if (state == 2 && line.charAt(0) == 's') {
				var m, t = line.split(/\s+/);
				if ((m = /S(\d+)_\d+/.exec(t[1])) == null) throw Error("Failed to parse the read name");
				var chr_id = parseInt(m[1]) - 1;
				if (chr_id >= chr_list.length) throw Error("Index outside the chr list");
				var name = [t[1], chr_list[chr_id], reg[0], reg[1], t[4]].join("!");
				var seq = t[6].replace(/\-/g, "");
				if (seq.length != parseInt(t[5])) throw Error("Inconsistent read length");
				if (seq.indexOf("NN") < 0) {
					if (t[4] == '-') {
						buf2.set(seq, 0);
						buf2.length = seq.length;
						buf2.revcomp();
						seq = buf2.toString();
					}
					print(">" + name);
					print(seq);
				}
				state = 0;
			}
		}
		file.close();
	}
	buf.destroy();
	buf2.destroy();
}

function paf_junceval(args)
{
	var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false;
	while ((c = getopt(args, "l:epc")) != null) {
		if (c == 'l') l_fuzzy = parseInt(getopt.arg);
		else if (c == 'e') print_err_only = print_ovlp = true;
		else if (c == 'p') print_ovlp = true;
		else if (c == 'c') chr_only = true;
	}

	if (args.length - getopt.ind < 1) {
		print("Usage: paftools.js junceval [options] <gene.gtf> <aln.sam>");
		print("Options:");
		print("  -l INT    tolerance of junction positions (0 for exact) [0]");
		print("  -p        print overlapping introns");
		print("  -e        print erroreous overlapping introns");
		print("  -c        only consider alignments to /^(chr)?([0-9]+|X|Y)$/");
		exit(1);
	}

	var file, buf = new Bytes();

	var tr = {};
	file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
	while (file.readline(buf) >= 0) {
		var m, t = buf.toString().split("\t");
		if (t[0].charAt(0) == '#') continue;
		if (t[2] != 'exon') continue;
		var st = parseInt(t[3]) - 1;
		var en = parseInt(t[4]);
		if ((m = /transcript_id "(\S+)"/.exec(t[8])) == null) continue;
		var tid = m[1];
		if (tr[tid] == null) tr[tid] = [t[0], t[6], 0, 0, []];
		tr[tid][4].push([st, en]);
	}
	file.close();

	var anno = {};
	for (var tid in tr) {
		var t = tr[tid];
		Interval.sort(t[4]);
		t[2] = t[4][0][0];
		t[3] = t[4][t[4].length - 1][1];
		if (anno[t[0]] == null) anno[t[0]] = [];
		var s = t[4];
		for (var i = 0; i < s.length - 1; ++i) {
			if (s[i][1] >= s[i+1][0])
				warn("WARNING: incorrect annotation for transcript "+tid+" ("+s[i][1]+" >= "+s[i+1][0]+")")
					anno[t[0]].push([s[i][1], s[i+1][0]]);
		}
	}
	tr = null;

	for (var chr in anno) {
		var e = anno[chr];
		if (e.length == 0) continue;
		Interval.sort(e);
		var k = 0;
		for (var i = 1; i < e.length; ++i) // dedup
			if (e[i][0] != e[k][0] || e[i][1] != e[k][1])
				e[++k] = e[i].slice(0);
		e.length = k + 1;
		Interval.index_end(e);
	}

	var n_pri = 0, n_unmapped = 0, n_mapped = 0;
	var n_sgl = 0, n_splice = 0, n_splice_hit = 0, n_splice_novel = 0;

	file = getopt.ind+1 >= args.length || args[getopt.ind+1] == '-'? new File() : new File(args[getopt.ind+1]);
	var last_qname = null;
	var re_cigar = /(\d+)([MIDNSHX=])/g;
	while (file.readline(buf) >= 0) {
		var m, t = buf.toString().split("\t");

		if (t[0].charAt(0) == '@') continue;
		if (chr_only && !/^(chr)?([0-9]+|X|Y)$/.test(t[2])) continue;
		var flag = parseInt(t[1]);
		if (flag&0x100) continue;
		if (first_only && last_qname == t[0]) continue;
		if (t[2] == '*') {
			++n_unmapped;
			continue;
		} else {
			++n_pri;
			if (last_qname != t[0]) {
				++n_mapped;
				last_qname = t[0];
			}
		}

		var pos = parseInt(t[3]) - 1, intron = [];
		while ((m = re_cigar.exec(t[5])) != null) {
			var len = parseInt(m[1]), op = m[2];
			if (op == 'N') {
				intron.push([pos, pos + len]);
				pos += len;
			} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') pos += len;
		}
		if (intron.length == 0) {
			++n_sgl;
			continue;
		}
		n_splice += intron.length;

		var chr = anno[t[2]];
		if (chr != null) {
			for (var i = 0; i < intron.length; ++i) {
				var o = Interval.find_ovlp(chr, intron[i][0], intron[i][1]);
				if (o.length > 0) {
					var hit = false;
					for (var j = 0; j < o.length; ++j) {
						var st_diff = intron[i][0] - o[j][0];
						var en_diff = intron[i][1] - o[j][1];
						if (st_diff < 0) st_diff = -st_diff;
						if (en_diff < 0) en_diff = -en_diff;
						if (st_diff <= l_fuzzy && en_diff <= l_fuzzy)
							++n_splice_hit, hit = true;
						if (hit) break;
					}
					if (print_ovlp) {
						var type = hit? 'C' : 'P';
						if (hit && print_err_only) continue;
						var x = '[';
						for (var j = 0; j < o.length; ++j) {
							if (j) x += ', ';
							x += '(' + o[j][0] + "," + o[j][1] + ')';
						}
						x += ']';
						print(type, t[0], i+1, t[2], intron[i][0], intron[i][1], x);
					}
				} else {
					++n_splice_novel;
					if (print_ovlp)
						print('N', t[0], i+1, t[2], intron[i][0], intron[i][1]);
				}
			}
		} else {
			n_splice_novel += intron.length;
		}
	}
	file.close();

	buf.destroy();

	if (!print_ovlp) {
		print("# unmapped reads: " + n_unmapped);
		print("# mapped reads: " + n_mapped);
		print("# primary alignments: " + n_pri);
		print("# singletons: " + n_sgl);
		print("# predicted introns: " + n_splice);
		print("# non-overlapping introns: " + n_splice_novel);
		print("# correct introns: " + n_splice_hit + " (" + (n_splice_hit / n_splice * 100).toFixed(2) + "%)");
	}
}

// evaluate overlap sensitivity
function paf_ov_eval(args)
{
	var c, min_ovlp = 2000, min_frac = 0.95, min_mapq = 10;
	while ((c = getopt(args, "q:l:f:")) != null) {
		if (c == 'q') min_mapq = parseInt(getopt.arg);
		else if (c == 'l') min_ovlp = parseInt(getopt.arg);
		else if (c == 'f') min_frac = parseFloat(getopt.arg);
	}
	if (args.length - getopt.ind < 2) {
		print("Usage: sort -k6,6 -k8,8n to-ref.paf | paftools.js ov-eval [options] - <ovlp.paf>");
		print("Options:");
		print("  -l INT     min overlap length [2000]");
		print("  -q INT     min mapping quality [10]");
		print("  -f FLOAT   min fraction of mapped length [0.95]");
		exit(1);
	}

	var buf = new Bytes();
	var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
	var a = [], h = {};
	while (file.readline(buf) >= 0) {
		var t = buf.toString().split("\t");
		var is_pri = false;
		if (parseInt(t[11]) < min_mapq) continue;
		for (var i = 12; i < t.length; ++i)
			if (t[i] == 'tp:A:P')
				is_pri = true;
		if (!is_pri) continue;
		for (var i = 1; i <= 3; ++i)
			t[i] = parseInt(t[i]);
		for (var i = 6; i <= 8; ++i)
			t[i] = parseInt(t[i]);
		if (t[3] - t[2] < min_ovlp || t[8] - t[7] < min_ovlp || (t[3] - t[2]) / t[1] < min_frac)
			continue;
		var ctg = t[5], st = t[7], en = t[8];
		while (a.length > 0) {
			if (a[0][0] == ctg && a[0][2] > st)
				break;
			else a.shift();
		}
		for (var j = 0; j < a.length; ++j) {
			if (a[j][3] == t[0]) continue;
			var len = (en > a[j][2]? a[j][2] : en) - st;
			if (len >= min_ovlp) {
				var key = a[j][3] < t[0]? a[j][3] + "\t" + t[0] : t[0] + "\t" + a[j][3];
				h[key] = len;
			}
		}
		a.push([ctg, st, en, t[0]]);
	}
	file.close();

	file = new File(args[getopt.ind + 1]);
	while (file.readline(buf) >= 0) {
		var t = buf.toString().split("\t");
		var key = t[0] < t[5]? t[0] + "\t" + t[5] : t[5] + "\t" + t[0];
		if (h[key] > 0) h[key] = -h[key];
	}
	file.close();
	buf.destroy();

	var n_ovlp = 0, n_missing = 0;
	for (var key in h) {
		++n_ovlp;
		if (h[key] > 0) ++n_missing;
	}
	print(n_ovlp + " overlaps inferred from the reference mapping");
	print(n_missing + " missed by the read overlapper");
	print((100 * (1 - n_missing / n_ovlp)).toFixed(2) + "% sensitivity");
}

/*************************
 ***** main function *****
 *************************/

function main(args)
{
	if (args.length == 0) {
		print("Usage: paftools.js <command> [arguments]");
		print("Commands:");
		print("  view       convert PAF to BLAST-like (for eyeballing) or MAF");
		print("  splice2bed convert spliced alignment in PAF/SAM to BED12");
		print("  sam2paf    convert SAM to PAF");
		print("  delta2paf  convert MUMmer's delta to PAF");
		print("  gff2bed    convert GTF/GFF3 to BED12");
		print("");
		print("  stat       collect basic mapping information in PAF/SAM");
		print("  liftover   simplistic liftOver");
		print("  call       call variants from asm-to-ref alignment with the cs tag");
		print("  bedcov     compute the number of bases covered");
		print("  version    print paftools.js version");
		print("");
		print("  mapeval    evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ");
		print("  mason2fq   convert mason2-simulated SAM to FASTQ");
		print("  pbsim2fq   convert PBSIM-simulated MAF to FASTQ");
		print("  junceval   evaluate splice junction consistency with known annotations");
		print("  ov-eval    evaluate read overlap sensitivity using read-to-ref mapping");
		exit(1);
	}

	var cmd = args.shift();
	if (cmd == 'view') paf_view(args);
	else if (cmd == 'sam2paf') paf_sam2paf(args);
	else if (cmd == 'delta2paf') paf_delta2paf(args);
	else if (cmd == 'splice2bed') paf_splice2bed(args);
	else if (cmd == 'gff2bed') paf_gff2bed(args);
	else if (cmd == 'stat') paf_stat(args);
	else if (cmd == 'liftover' || cmd == 'liftOver') paf_liftover(args);
	else if (cmd == 'call') paf_call(args);
	else if (cmd == 'mapeval') paf_mapeval(args);
	else if (cmd == 'bedcov') paf_bedcov(args);
	else if (cmd == 'mason2fq') paf_mason2fq(args);
	else if (cmd == 'pbsim2fq') paf_pbsim2fq(args);
	else if (cmd == 'junceval') paf_junceval(args);
	else if (cmd == 'ov-eval') paf_ov_eval(args);
	else if (cmd == 'version') print(paftools_version);
	else throw Error("unrecognized command: " + cmd);
}

main(arguments);