minimap2 0.2.28.0 → 0.2.29.0

data/ext/minimap2/misc/mmphase.js

@@ -1,335 +0,0 @@
-#!/usr/bin/env k8
-
-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 read_fastx(file, buf)
-{
-	if (file.readline(buf) < 0) return null;
-	var m, line = buf.toString();
-	if ((m = /^([>@])(\S+)/.exec(line)) == null)
-		throw Error("wrong fastx format");
-	var is_fq = (m[1] == '@');
-	var name = m[2];
-	if (file.readline(buf) < 0)
-		throw Error("missing sequence line");
-	var seq = buf.toString();
-	if (is_fq) { // skip quality
-		file.readline(buf);
-		file.readline(buf);
-	}
-	return [name, seq];
-}
-
-function filter_paf(a, opt)
-{
-	if (a.length == 0) return;
-	var k = 0;
-	for (var i = 0; i < a.length; ++i) {
-		var ai = a[i];
-		if (ai[10] < opt.min_blen) continue;
-		if (ai[9] < ai[10] * opt.min_iden) continue;
-		var clip = [0, 0];
-		if (ai[4] == '+') {
-			clip[0] = ai[2] < ai[7]? ai[2] : ai[7];
-			clip[1] = ai[1] - ai[3] < ai[6] - ai[8]? ai[1] - ai[3] : ai[6] - ai[8];
-		} else {
-			clip[0] = ai[2] < ai[6] - ai[8]? ai[2] : ai[6] - ai[8];
-			clip[1] = ai[1] - ai[3] < ai[7]? ai[1] - ai[3] : ai[7];
-		}
-		if (clip[0] > opt.max_clip_len || clip[1] > opt.max_clip_len) continue;
-		a[k++] = ai;
-	}
-	a.length = k;
-}
-
-function parse_events(t, ev, id, buf)
-{
-	var re = /(:(\d+))|(([\+\-\*])([a-z]+))/g;
-	var m, cs = null;
-	for (var j = 12; j < t.length; ++j) {
-		if ((m = /^cs:Z:(\S+)/.exec(t[j])) != null) {
-			cs = m[1].toLowerCase();
-			break;
-		}
-	}
-	if (cs == null) {
-		warn("Warning: no cs tag for read '" + t[0] + "'");
-		return;
-	}
-	var st = t[2], en = t[3];
-	var x = st;
-	while ((m = re.exec(cs)) != null) {
-		var l;
-		if (m[2] != null) { // an identitcal match ":\d+"
-			l = parseInt(m[2]);
-			// [start, end, type, index, changed_base]
-			ev.push([x, x + l, 0, id]);
-		} else {
-			if (m[4] == '*') {
-				l = 1;
-				ev.push([x, x + 1, 1, id, m[5][0]]);
-			} else if (m[4] == '+') {
-				l = m[5].length;
-				ev.push([x, x + l, 2, id]);
-			} else if (m[4] == '-') {
-				l = 0;
-				ev.push([x, x, -1, id, m[5]]);
-			}
-		}
-		x += l;
-	}
-	if (x != en)
-		throw Error("inconsistent cs for read '" + t[0] + "'");
-}
-
-function find_het_sub(ev, a, opt)
-{
-	var n = a.length, last0_i = -1, h = [], d = [];
-	for (var i = 0; i < n; ++i) h[i] = [], d[i] = [];
-	for (var i = 0; i < ev.length; ++i) {
-		if (ev[i][2] == 0) {
-			if (last0_i < 0 || ev[i][0] != ev[last0_i][0]) last0_i = i;
-			else if (ev[i][1] > ev[last0_i][1])
-				last0_i = i;
-		} else if (ev[i][2] == 1 && last0_i >= 0 && ev[i][0] < ev[last0_i][1]) {
-			if (ev[last0_i][1] - ev[last0_i][0] >= opt.min_mlen) {
-				if (opt.dbg_ev) print("EV", ev[last0_i].join("\t"), "|", ev[i].join("\t"));
-				var e0 = ev[last0_i], hl = h[e0[3]];
-				if (hl.length == 0 || hl[hl.length-1][0] != e0[0])
-					hl.push([e0[0], e0[1]]);
-				d[ev[i][3]].push([ev[i][0], e0[1] - e0[0]]);
-			}
-		}
-	}
-	var b = [];
-	for (var i = 0; i < n; ++i) {
-		var sh = 0, dh = 0;
-		for (var j = 0; j < h[i].length; ++j)
-			sh += h[i][j][1] - h[i][j][0];
-		for (var j = 0; j < d[i].length; ++j)
-			dh += d[i][j][1];
-		// [start, end, index, #consistent, lenConsistent, #conflictive, lenConflictive, identity, mlen]
-		b[i] = [a[i][2], a[i][3], i, h[i].length, sh, d[i].length, dh, a[i][9] / a[i][10], a[i][9]];
-	}
-	return b;
-}
-
-function flt_utg_for_ec(b, opt)
-{
-	var k = 0;
-	for (var i = 0; i < b.length; ++i) {
-		var bi = b[i];
-		if (bi[4] == 0 && bi[6] == 0) b[k++] = bi; // entirely ambiguous
-		else if (bi[6] < (bi[4] + bi[6]) * opt.max_ratio0) b[k++] = bi;
-	}
-	b.length = k;
-	if (b.length == 0) return;
-	// find the longest contiguous segment
-	b.sort(function(x,y) { return x[0]-y[0] });
-	var st = b[0][0], en = b[0][1], max_st = 0, max_en = 0, max_max_en = en;
-	for (var i = 1; i < b.length; ++i) {
-		if (b[i][0] > en) {
-			if (en - st > max_en - max_st)
-				max_st = st, max_en = en;
-			st = b[i][0], en = b[i][1];
-		} else {
-			en = en > b[i][1]? en : b[i][1];
-		}
-		max_max_en = max_max_en > b[i][1]? max_max_en : b[i][1];
-	}
-	if (en - st > max_en - max_st)
-		max_st = st, max_en = en;
-	if (max_max_en != en || st != b[0][0]) {
-		var k = 0;
-		for (var i = 0; i < b.length; ++i)
-			if (b[i][0] < max_en && b[i][1] > max_st)
-				b[k++] = b[i];
-		b.length = k;
-	}
-}
-
-function flt_utg_for_bin(b, opt) // filter out alignments clearly on the wrong phase
-{
-	var k = 0;
-	for (var i = 0; i < b.length; ++i) {
-		var bi = b[i];
-		if (bi[4] + bi[6] == 0 || bi[4] >= (bi[4] + bi[6]) * opt.max_ratio0) b[k++] = bi;
-	}
-	b.length = k;
-}
-
-function ec_core(b, n_a, ev, buf, ecb) // error correction
-{
-	var intv = [];
-	for (var i = 0; i < n_a; ++i)
-		intv[i] = null;
-	intv[b[0][2]] = [b[0][0], b[0][1]];
-	var en = b[0][1];
-	for (var i = 1; i < b.length; ++i) {
-		if (b[i][1] <= en) continue;
-		intv[b[i][2]] = [en, b[i][1]];
-		en = b[i][1];
-	}
-	var k = 0;
-	ecb.capacity = buf.capacity;
-	ecb.length = 0;
-	for (var i = 0; i < ev.length; ++i) {
-		var e = ev[i], I = intv[e[3]];
-		if (I == null) continue;
-		if (e[0] >= I[0] && e[0] < I[1]) { // this is to reduce duplicated events around junctions
-			//print("X", e.join("\t"));
-			if (e[2] == 0) {
-				ecb.length += e[1] - e[0];
-				for (var j = e[0]; j < e[1]; ++j)
-					ecb[k++] = buf[j];
-			} else if (e[2] == 1) {
-				++ecb.length;
-				ecb[k++] = e[4].charCodeAt(0);
-			} else if (e[2] < 0) {
-				ecb.length += e[4].length;
-				for (var j = 0; j < e[4].length; ++j)
-					ecb[k++] = e[4].charCodeAt(j);
-			} // else, skip e[2] == 2
-		}
-	}
-	if (ecb.length != k) throw Error("BUG!");
-}
-
-function process_paf(a, opt, fp_seq, buf, ecb)
-{
-	if (a.length == 0) return;
-	var len = a[0][1], name = a[0][0], seq = null;
-	if (len < opt.min_rlen) return;
-	if (fp_seq) {
-		var ret;
-		while ((ret = read_fastx(fp_seq, buf)) != null)
-			if (ret[0] == a[0][0])
-				break;
-		if (ret == null)
-			throw Error("failed to find sequence for read '" + a[0][0] + "'");
-		name = ret[0], seq = ret[1];
-		if (seq.length != len)
-			throw Error("inconsistent length for read '" + name + "'");
-	}
-	filter_paf(a, opt);
-	if (a.length == 0) return;
-	var ev = [];
-	for (var i = 0; i < a.length; ++i)
-		parse_events(a[i], ev, i, buf);
-	ev.sort(function(x,y) { return x[0]!=y[0]? x[0]-y[0] : x[2]-y[2] });
-	if (seq == null) print("SQ", name, a[0][1], a.length);
-	var b = find_het_sub(ev, a, opt);
-	if (opt.ec) flt_utg_for_ec(b, opt);
-	else flt_utg_for_bin(b, opt);
-	if (seq == null) {
-		for (var i = 0; i < b.length; ++i) {
-			var m, ai = a[b[i][2]], score = 0;
-			for (var j = 10; j < ai.length; ++j)
-				if ((m = /^AS:i:(\d+)/.exec(ai[j])) != null)
-					score = m[1];
-			print("TS", b[i][2], b[i][0], b[i][1], ai.slice(5, 9).join("\t"), b[i].slice(3, 7).join("\t"), score);
-		}
-		print("//");
-	} else { // error correction
-		if (b.length == 0) return;
-		buf.set(seq, 0);
-		ec_core(b, a.length, ev, buf, ecb);
-		print(">" + name);
-		print(ecb);
-	}
-}
-
-function main(args)
-{
-	var c, opt = { min_rlen:5000, min_blen:5000, min_iden:0.8, min_mlen:5, max_clip_len:500, max_ratio0:0.25, dbg_ev:false };
-	while ((c = getopt(args, "l:b:d:m:c:r:E")) != null) {
-		if (c == 'l') opt.min_rlen = parseInt(getopt.arg);
-		else if (c == 'b') opt.min_blen = parseInt(getopt.arg);
-		else if (c == 'd') opt.min_iden = parseFloat(getopt.arg);
-		else if (c == 'm') opt.min_slen = parseInt(getopt.arg);
-		else if (c == 'c') opt.max_clip_len = parseInt(getopt.arg);
-		else if (c == 'r') opt.max_ratio0 = parseFloat(getopt.arg);
-		else if (c == 'E') opt.dbg_ev = true;
-	}
-	if (args.length - getopt.ind < 1) {
-		print("Usage: mmphase.js [options] <map-with-cs.paf> [reads.fa]");
-		print("Options:");
-		print("  -l INT    min read length [" + opt.min_rlen + "]");
-		print("  -b INT    min alignment length [" + opt.min_blen + "]");
-		print("  -d FLOAT  min identity [" + opt.min_iden + "]");
-		print("  -s INT    min match length [" + opt.min_mlen + "]");
-		print("  -c INT    max clip length [" + opt.max_clip_len + "]");
-		print("  -r FLOAT  initial ratio for haplotype filtering [" + opt.max_ratio0 + "]");
-		return 0;
-	}
-
-	opt.ec = args.length - getopt.ind < 2? false : true;
-	if (!opt.ec) {
-		print("CC");
-		print("CC", "SQ  qName  qLen    nHits");
-		print("CC", "TS  index  qStart  qEnd  tName  tLen  tStart  tEnd  nConsistent  lCons  nConflictive  lConf  score");
-		print("CC");
-	}
-
-	var buf = new Bytes(), ecb = new Bytes();
-	var fp_paf = new File(args[getopt.ind]);
-	var fp_seq = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : null;
-	var a = [];
-	while (fp_paf.readline(buf) >= 0) {
-		var t = buf.toString().split("\t");
-		if (a.length > 0 && a[0][0] != t[0]) {
-			process_paf(a, opt, fp_seq, buf, ecb);
-			a.length = 0;
-		}
-		for (var i = 1; i <= 3; ++i) t[i] = parseInt(t[i]);
-		if (t[1] < opt.min_rlen) continue;
-		for (var i = 6; i <= 10; ++i) t[i] = parseInt(t[i]);
-		if (t[10] < opt.min_blen) continue;
-		a.push(t);
-	}
-	if (a.length >= 0)
-		process_paf(a, opt, fp_seq, buf, ecb);
-	if (fp_seq) fp_seq.close();
-	fp_paf.close();
-	ecb.destroy();
-	buf.destroy();
-}
-
-var ret = main(arguments)
-exit(ret)