code backup
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Heng Li
parent
ce3c198245
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024195db62
239
bwa-helper.js
239
bwa-helper.js
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@ -2,7 +2,7 @@
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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: https://sourceforge.net/projects/lh3/files/ *
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* Binary: http://sourceforge.net/projects/lh3/files/k8/ *
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*****************************************************************/
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/******************
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@ -338,6 +338,242 @@ 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, is_contained) {
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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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if (!is_contained) {
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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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} else {
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for (var i = off; i < intv.length && intv[i][1] <= _e; ++i)
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if (intv[i][0] >= _b) ovlp.push(intv[i]);
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}
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return ovlp;
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}
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}
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function bwa_genalt(args)
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{
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function cigar2pos(cigar, pos)
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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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var opt = { a:1, b:4, o:6, e:1 };
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if (args.length == 0) {
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print("Usage: k8 bwa-helper.js genalt <alt.sam> [aln.sam]");
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exit(1);
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}
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var re_cigar = /(\d+)([MIDSHN])/g;
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var file, buf = new Bytes();
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// read the ALT-to-REF alignment and generate the index
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var intv = {};
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file = new File(args[0]);
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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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file.close();
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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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// process SAM
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file = args.length >= 2? new File(args[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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//print(line);
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continue;
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}
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// parse 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 : parseInt(m[1]);
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var t = line.split("\t");
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// a hit element: [0:chr, 1:isRev, 2:start, 3:end, 4:cigar, 5:NM, 6:score, 7+:"lifted info"]
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var hits = [[t[2], (parseInt(t[1]) & 16)? true : false, parseInt(t[3]) - 1, 0, t[5], NM]]; // the major hit
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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] == '') continue; // if the last char is ';', we will have an empty string
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var s = XA_strs[i].split(",");
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hits.push([s[0], s[1].charAt(0) == '-'? true : false, parseInt(s[1].substr(1)) - 1, 0, s[2], parseInt(s[3])]);
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}
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// lift mapping positions to the 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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// parse the cigar
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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[4])) != 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') l_clip += l;
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}
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h[3] = h[2] + l_match + l_del + l_skip;
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h[5] = h[5] > l_del + l_ins? h[5] : l_del + l_ins;
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var score = opt.a * l_match - (opt.a + opt.b) * (h[5] - l_del - l_ins) - opt.o * (n_del + n_ins) - opt.e * (l_del + l_ins);
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h.push(score);
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if (idx[h[0]] == null) continue;
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var a = idx[h[0]](h[2], h[3]);
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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 regs = [];
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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[2]);
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e = cigar2pos(a[j][6], h[3] - 1) + 1;
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} else {
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s = cigar2pos(a[j][6], a[j][2] - h[3]);
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e = cigar2pos(a[j][6], a[j][2] - h[2] - 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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//print("*", a[j][4], h[0], a[j][3], s, e);
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regs.push([a[j][3], (h[1]!=a[j][4]), s, e]);
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}
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if (regs.length == 0) continue;
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hits[i].push(regs[0][0], regs[0][1], regs[0][2], regs[0][3]); // TODO: regs.length may be larger than one, though this occurs rarely
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++n_lifted;
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}
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if (n_lifted == 0) {
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//print(line);
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continue;
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}
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// group hits
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var phits = [];
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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 (h.length > 7) phits.push([h[7], h[9], h[10], -1]); // lifted
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else phits.push([h[0], h[2], h[3], -1]);
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}
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phits.sort(function(a,b) {
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if (a[0] != b[0]) return a[0] < b[0]? -1 : 1;
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if (a[1] != b[1]) return a[1] - b[1];
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});
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var last_chr = null, end = 0, groupid = -1;
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for (var i = 0; i < phits.length; ++i) {
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if (last_chr != phits[i][0]) { // change of chr
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phits[i][3] = ++groupid;
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last_chr = phits[i][0], end = phits[i][2];
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} else if (phits[i][1] >= end) { // no overlap
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phits[i][3] = ++groupid;
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end = phits[i][2];
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} else {
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phits[i][3] = groupid;
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end = end > phits[i][2]? end : phits[i][2];
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}
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}
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var n_group0 = 0; // #hits overlapping the reported hit
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for (var i = 0; i < phits.length; ++i)
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if (phits[i][3] == phits[0][3])
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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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//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 < phits.length; ++i)
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if (group_max[phits[i][3]] == null || group_max[phits[i][3]][0] < hits[i][6])
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group_max[phits[i][3]] = [hits[i][6], phits[i][3]];
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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] == phits[0][3]) { // 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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t[4] = mapQ;
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print(t.join("\t"));
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print("*", mapQ);
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for (var i = 0; i < hits.length; ++i)
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print(hits[i]);
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}
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file.close();
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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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@ -362,6 +598,7 @@ 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 == 'genalt') bwa_genalt(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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