separate postalt to a separate script
This commit is contained in:
Heng Li
parent
23bc50e240
commit
a33ca20499
353
bwa-helper.js
353
bwa-helper.js
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@ -51,60 +51,6 @@ var getopt = function(args, ostr) {
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return optopt;
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}
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function obj2str(o)
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{
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if (typeof(o) != 'object') {
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return o.toString();
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} else if (o == null) {
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return "null";
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} else if (Array.isArray(o)) {
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var s = "[";
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for (var i = 0; i < o.length; ++i) {
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if (i) s += ',';
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s += obj2str(o[i]);
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}
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return s + "]";
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} else {
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var i = 0, s = "{";
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for (var key in o) {
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if (i++) s += ',';
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s += key + ":";
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s += obj2str(o[key]);
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}
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return s + "}";
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}
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}
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Bytes.prototype.reverse = function()
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{
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for (var i = 0; i < this.length>>1; ++i) {
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var tmp = this[i];
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this[i] = this[this.length - i - 1];
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this[this.length - i - 1] = tmp;
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}
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}
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Bytes.prototype.revcomp = function()
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{
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if (Bytes.rctab == null) {
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var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
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var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
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Bytes.rctab = [];
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for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
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for (var i = 0; i < s1.length; ++i)
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Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
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}
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for (var i = 0; i < this.length>>1; ++i) {
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var tmp = this[this.length - i - 1];
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this[this.length - i - 1] = Bytes.rctab[this[i]];
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this[i] = Bytes.rctab[tmp];
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}
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if (this.length>>1)
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this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
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}
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var re_cigar = /(\d+)([MIDSHN])/g;
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/************************
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*** command markovlp ***
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************************/
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@ -396,301 +342,6 @@ function bwa_gff2sam(args)
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file.close();
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}
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/******************************
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*** Generate ALT alignment ***
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******************************/
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function intv_ovlp(intv, bits) // interval index
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{
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if (typeof bits == "undefined") bits = 13;
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intv.sort(function(a,b) {return a[0]-b[0];});
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// create the index
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var idx = [], max = 0;
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for (var i = 0; i < intv.length; ++i) {
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var b = intv[i][0]>>bits;
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var e = (intv[i][1]-1)>>bits;
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if (b != e) {
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for (var j = b; j <= e; ++j)
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if (idx[j] == null) idx[j] = i;
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} else if (idx[b] == null) idx[b] = i;
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max = max > e? max : e;
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}
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// closure
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return function(_b, _e) {
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var x = _b >> bits;
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if (x > max) return [];
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var off = idx[x];
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if (off == null) {
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var i;
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for (i = ((_e - 1) >> bits) - 1; i >= 0; --i)
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if (idx[i] != null) break;
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off = i < 0? 0 : idx[i];
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}
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var ovlp = [];
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for (var i = off; i < intv.length && intv[i][0] < _e; ++i)
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if (intv[i][1] > _b) ovlp.push(intv[i]);
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return ovlp;
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}
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}
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function cigar2pos(cigar, pos) // given a pos on ALT and the ALT-to-REF CIGAR, find the pos on REF
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{
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var x = 0, y = 0;
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for (var i = 0; i < cigar.length; ++i) {
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var op = cigar[i][0], len = cigar[i][1];
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if (op == 'M') {
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if (y <= pos && pos < y + len)
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return x + (pos - y);
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x += len, y += len;
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} else if (op == 'D') {
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x += len;
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} else if (op == 'I') {
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if (y <= pos && pos < y + len)
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return x;
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y += len;
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} else if (op == 'S' || op == 'H') {
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if (y <= pos && pos < y + len)
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return -1;
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y += len;
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}
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}
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return -1;
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}
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function parse_hit(s, opt) // parse a hit. s looks something like ["chr1", "+12345", "100M", 5]
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{
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var h = {};
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h.ctg = s[0];
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h.start = parseInt(s[1].substr(1)) - 1;
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h.rev = (s[1].charAt(0) == '-');
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h.cigar = s[2];
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h.NM = parseInt(s[3]);
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h.hard = false;
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var m, l_ins, n_ins, l_del, n_del, l_match, l_skip, l_clip;
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l_ins = l_del = n_ins = n_del = l_match = l_skip = l_clip = 0;
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while ((m = re_cigar.exec(h.cigar)) != null) {
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var l = parseInt(m[1]);
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if (m[2] == 'M') l_match += l;
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else if (m[2] == 'D') ++n_del, l_del += l;
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else if (m[2] == 'I') ++n_ins, l_ins += l;
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else if (m[2] == 'N') l_skip += l;
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else if (m[2] == 'H' || m[2] == 'S') {
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l_clip += l;
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if (m[2] == 'H') h.hard = true;
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}
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}
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h.end = h.start + l_match + l_del + l_skip;
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h.NM = h.NM > l_del + l_ins? h.NM : l_del + l_ins;
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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);
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h.l_query = l_match + l_ins + l_clip;
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return h;
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}
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// read the ALT-to-REF alignment and generate the index
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function read_ALT_sam(fn)
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{
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var intv = {};
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var file = new File(fn);
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var buf = new Bytes();
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while (file.readline(buf) >= 0) {
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var line = buf.toString();
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var t = line.split("\t");
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if (line.charAt(0) == '@') continue;
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var flag = parseInt(t[1]);
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var m, cigar = [], l_qaln = 0, l_qclip = 0;
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while ((m = re_cigar.exec(t[5])) != null) {
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var l = parseInt(m[1]);
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cigar.push([m[2] != 'H'? m[2] : 'S', l]); // convert hard clip to soft clip
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if (m[2] == 'M' || m[2] == 'I') l_qaln += l;
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else if (m[2] == 'S' || m[2] == 'H') l_qclip += l;
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}
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var j = flag&16? cigar.length-1 : 0;
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var start = cigar[j][0] == 'S'? cigar[j][1] : 0;
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if (intv[t[0]] == null) intv[t[0]] = [];
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intv[t[0]].push([start, start + l_qaln, l_qaln + l_qclip, t[2], flag&16? true : false, parseInt(t[3]) - 1, cigar]);
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//print(start, start + l_qaln, t[2], flag&16? true : false, parseInt(t[3]), cigar);
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}
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buf.destroy();
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file.close();
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// create the interval index
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var idx = {};
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for (var ctg in intv)
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idx[ctg] = intv_ovlp(intv[ctg]);
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return idx;
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}
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function bwa_altgen(args)
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{
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var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false };
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while ((c = getopt(args, 'pv:')) != null) {
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if (c == 'v') opt.verbose = parseInt(getopt.arg);
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else if (c == 'p') opt.show_pri = true;
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}
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if (args.length == getopt.ind) {
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print("Usage: k8 bwa-helper.js altgen [-p] <alt.sam> [aln.sam]");
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exit(1);
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}
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var file, buf = new Bytes();
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var aux = new Bytes(); // used for reverse and reverse complement
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var idx = read_ALT_sam(args[getopt.ind]);
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// process SAM
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file = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : new File();
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while (file.readline(buf) >= 0) {
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var m, line = buf.toString();
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if (line.charAt(0) == '@' || (m = /\tXA:Z:(\S+)/.exec(line)) == null) { // TODO: this does not work with PE file
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if (opt.verbose < 4) print(line);
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continue;
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}
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// parse hits
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var hits = [];
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var XA_strs = m[1].split(";");
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var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
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var t = line.split("\t");
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var flag = parseInt(t[1]);
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var h = parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt);
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if (h.hard) { // the following does not work with hard clipped SEQ
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print(line);
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continue;
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}
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hits.push(h);
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for (var i = 0; i < XA_strs.length; ++i) // hits in the XA tag
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if (XA_strs[i] != '') // as the last symbol in an XA tag is ";", the last split is an empty string
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hits.push(parse_hit(XA_strs[i].split(","), opt));
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// lift mapping positions to coordinates on the primary assembly
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var n_lifted = 0;
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for (var i = 0; i < hits.length; ++i) {
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var h = hits[i];
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if (idx[h.ctg] == null) continue;
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var a = idx[h.ctg](h.start, h.end);
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if (a == null || a.length == 0) continue;
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// find the approximate position on the primary assembly
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var lifted = [];
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for (var j = 0; j < a.length; ++j) {
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var s, e;
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if (!a[j][4]) { // ALT is mapped to the forward strand of the primary assembly
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s = cigar2pos(a[j][6], h.start);
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e = cigar2pos(a[j][6], h.end - 1) + 1;
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} else {
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s = cigar2pos(a[j][6], a[j][2] - h.end);
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e = cigar2pos(a[j][6], a[j][2] - h.start - 1) + 1;
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}
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if (s < 0 || e < 0) continue; // read is mapped to clippings in the ALT-to-chr alignment
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s += a[j][5]; e += a[j][5];
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lifted.push([a[j][3], (h.rev!=a[j][4]), s, e]);
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}
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if (lifted.length) ++n_lifted, hits[i].lifted = lifted;
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}
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if (n_lifted == 0) {
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if (opt.verbose < 4) print(line);
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continue;
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}
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// group hits
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for (var i = 0; i < hits.length; ++i) { // set keys for sorting
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if (hits[i].lifted && hits[i].lifted.length) // TODO: only the first element in lifted[] is used
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hits[i].pctg = hits[i].lifted[0][0], hits[i].pstart = hits[i].lifted[0][2], hits[i].pend = hits[i].lifted[0][3];
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else hits[i].pctg = hits[i].ctg, hits[i].pstart = hits[i].start, hits[i].pend = hits[i].end;
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hits[i].i = i; // keep the original index
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}
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hits.sort(function(a,b) { return a.pctg != b.pctg? (a.pctg < b.pctg? -1 : 1) : a.pstart - b.pstart });
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var last_chr = null, end = 0, g = -1;
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for (var i = 0; i < hits.length; ++i) {
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if (last_chr != hits[i].pctg) ++g, last_chr = hits[i].pctg, end = 0;
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else if (hits[i].pstart >= end) ++g;
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hits[i].g = g;
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end = end > hits[i].pend? end : hits[i].pend;
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}
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var reported_g = null, reported_i = null;
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for (var i = 0; i < hits.length; ++i)
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if (hits[i].i == 0)
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reported_g = hits[i].g, reported_i = i;
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var n_group0 = 0; // #hits overlapping the reported hit
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for (var i = 0; i < hits.length; ++i)
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if (hits[i].g == reported_g)
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++n_group0;
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if (n_group0 == 1) { // then keep the reported alignment and mapQ
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if (opt.verbose < 4) print(line);
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continue;
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}
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// re-estimate mapQ
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var group_max = [];
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for (var i = 0; i < hits.length; ++i) {
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var g = hits[i].g;
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if (group_max[g] == null || group_max[g][0] < hits[i].score)
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group_max[g] = [hits[i].score, g];
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}
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if (group_max.length > 1)
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group_max.sort(function(x,y) {return y[0]-x[0]});
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var mapQ;
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if (group_max[0][1] == reported_g) { // the best hit is the hit reported in SAM
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mapQ = group_max.length == 1? 60 : 6 * (group_max[0][0] - group_max[1][0]);
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} else mapQ = 0;
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mapQ = mapQ < 60? mapQ : 60;
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var ori_mapQ = parseInt(t[4]);
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mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ;
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// generate lifted_str
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for (var i = 0; i < hits.length; ++i) {
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if (hits[i].lifted && hits[i].lifted.length) {
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var lifted = hits[i].lifted;
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var u = '';
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for (var j = 0; j < lifted.length; ++j)
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u += lifted[j][0] + "," + lifted[j][2] + "," + lifted[j][3] + "," + (lifted[j][1]?'-':'+') + ";";
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hits[i].lifted_str = u;
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}
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}
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// generate reversed quality and reverse-complemented sequence if necessary
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var rs = null, rq = null; // reversed quality and reverse complement sequence
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var need_rev = false;
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for (var i = 0; i < hits.length; ++i) {
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if (hits[i].g != reported_g || i == reported_i) continue;
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if (hits[i].rev != hits[reported_i].rev)
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need_rev = true;
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}
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if (need_rev) { // reverse and reverse complement
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aux.set(t[9], 0); aux.revcomp(); rs = aux.toString();
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aux.set(t[10],0); aux.reverse(); rq = aux.toString();
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}
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// print
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t[4] = mapQ;
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t.push("om:i:"+ori_mapQ);
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if (hits[reported_i].lifted_str) t.push("lt:Z:" + hits[reported_i].lifted_str);
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print(t.join("\t"));
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var cnt = 0;
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for (var i = 0; i < hits.length; ++i) {
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if (opt.verbose >= 5) print(obj2str(hits[i]));
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if (hits[i].g != reported_g || i == reported_i) continue;
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if (!opt.show_pri && idx[hits[i].ctg] == null) continue;
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var s = [t[0], flag&0xf10, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0];
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// update name
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if (flag&0x40) s[0] += "/1";
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if (flag&0x80) s[0] += "/2";
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s[0] += "_" + (++cnt);
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if (hits[i].rev == hits[reported_i].rev) s.push(t[9], t[10]);
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else s.push(rs, rq);
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s.push("NM:i:" + hits[i].NM);
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if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);
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print(s.join("\t"));
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}
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}
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file.close();
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aux.destroy();
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buf.destroy();
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}
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/*********************
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*** Main function ***
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*********************/
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@ -699,8 +350,7 @@ function main(args)
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{
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if (args.length == 0) {
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print("\nUsage: k8 bwa-helper.js <command> [arguments]\n");
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print("Commands: altgen generate ALT alignments for ALT-unaware alignments");
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print(" sam2pas convert SAM to pairwise alignment summary format (PAS)");
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print("Commands: sam2pas convert SAM to pairwise alignment summary format (PAS)");
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print(" pas2reg extract covered regions");
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print(" reg2cut regions to extract for the 2nd round bwa-mem");
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print(" markovlp identify bi-directional overlaps");
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@ -716,7 +366,6 @@ function main(args)
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else if (cmd == 'markovlp') bwa_markOvlp(args);
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else if (cmd == 'pas2reg') bwa_pas2reg(args);
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else if (cmd == 'reg2cut') bwa_reg2cut(args);
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else if (cmd == 'altgen' || cmd == 'genalt') bwa_altgen(args);
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else if (cmd == 'shortname') bwa_shortname(args);
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else warn("Unrecognized command");
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}
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@ -0,0 +1,451 @@
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/*****************************************************************
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* The K8 Javascript interpreter is required to run this script. *
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* *
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* Source code: https://github.com/attractivechaos/k8 *
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* Binary: http://sourceforge.net/projects/lh3/files/k8/ *
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* *
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* Data file used for generating GRCh38 ALT alignments: *
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* *
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* http://sourceforge.net/projects/bio-bwa/files/ *
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*****************************************************************/
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/******************
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*** From k8.js ***
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******************/
|
||||
|
||||
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;
|
||||
if (n_group0 == 1) { // then keep the reported alignment and mapQ
|
||||
buf2.push(t);
|
||||
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 = t[4];
|
||||
mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ;
|
||||
|
||||
// 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;
|
||||
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);
|
||||
Loading…
Reference in New Issue