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genalt is working

This commit is contained in:
Heng Li 2014-05-06 16:02:40 -04:00
parent 8d37726325
commit c50ee8c841
1 changed files with 174 additions and 81 deletions
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255
bwa-helper.js
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@ -47,6 +47,58 @@ var getopt = function(args, ostr) {
return optopt; 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]];
}
/************************ /************************
*** command markovlp *** *** command markovlp ***
************************/ ************************/
@ -383,6 +435,8 @@ function intv_ovlp(intv, bits) // interval index
function bwa_genalt(args) function bwa_genalt(args)
{ {
var re_cigar = /(\d+)([MIDSHN])/g;
function cigar2pos(cigar, pos) function cigar2pos(cigar, pos)
{ {
var x = 0, y = 0; var x = 0, y = 0;
@ -407,19 +461,48 @@ function bwa_genalt(args)
return -1; return -1;
} }
var opt = { a:1, b:4, o:6, e:1 }; function parse_hit(s, opt)
{
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]);
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;
}
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;
}
if (args.length == 0) { var c, opt = { a:1, b:4, o:6, e:1, verbose:3 };
while ((c = getopt(args, 'v:')) != null) {
if (c == 'v') opt.verbose = parseInt(getopt.arg);
}
if (args.length == getopt.ind) {
print("Usage: k8 bwa-helper.js genalt <alt.sam> [aln.sam]"); print("Usage: k8 bwa-helper.js genalt <alt.sam> [aln.sam]");
exit(1); exit(1);
} }
var re_cigar = /(\d+)([MIDSHN])/g;
var file, buf = new Bytes(); var file, buf = new Bytes();
var aux = new Bytes();
// read the ALT-to-REF alignment and generate the index // read the ALT-to-REF alignment and generate the index
var intv = {}; var intv = {};
file = new File(args[0]); file = new File(args[getopt.ind]);
while (file.readline(buf) >= 0) { while (file.readline(buf) >= 0) {
var line = buf.toString(); var line = buf.toString();
var t = line.split("\t"); var t = line.split("\t");
@ -445,138 +528,147 @@ function bwa_genalt(args)
idx[ctg] = intv_ovlp(intv[ctg]); idx[ctg] = intv_ovlp(intv[ctg]);
// process SAM // process SAM
file = args.length >= 2? new File(args[1]) : new File(); file = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : new File();
while (file.readline(buf) >= 0) { while (file.readline(buf) >= 0) {
var m, line = buf.toString(); var m, line = buf.toString();
if (line.charAt(0) == '@' || (m = /\tXA:Z:(\S+)/.exec(line)) == null) { // TODO: this does not work with PE file if (line.charAt(0) == '@' || (m = /\tXA:Z:(\S+)/.exec(line)) == null) { // TODO: this does not work with PE file
//print(line); if (opt.verbose < 4) print(line);
continue; continue;
} }
// parse hits // parse hits
var hits = [];
var XA_strs = m[1].split(";"); var XA_strs = m[1].split(";");
var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? 0 : parseInt(m[1]); var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
var t = line.split("\t"); var t = line.split("\t");
// a hit element: [0:chr, 1:isRev, 2:start, 3:end, 4:cigar, 5:NM, 6:score, 7+:"lifted info"] var flag = parseInt(t[1]);
var hits = [[t[2], (parseInt(t[1]) & 16)? true : false, parseInt(t[3]) - 1, 0, t[5], NM]]; // the major hit hits.push(parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt));
for (var i = 0; i < XA_strs.length; ++i) { // hits in the XA tag for (var i = 0; i < XA_strs.length; ++i) // hits in the XA tag
if (XA_strs[i] == '') continue; // if the last char is ';', we will have an empty string if (XA_strs[i] != '')
var s = XA_strs[i].split(","); hits.push(parse_hit(XA_strs[i].split(","), opt));
hits.push([s[0], s[1].charAt(0) == '-'? true : false, parseInt(s[1].substr(1)) - 1, 0, s[2], parseInt(s[3])]);
}
// lift mapping positions to the coordinates on the primary assembly // lift mapping positions to the coordinates on the primary assembly
var n_lifted = 0; var n_lifted = 0;
for (var i = 0; i < hits.length; ++i) { for (var i = 0; i < hits.length; ++i) {
var h = hits[i]; var h = hits[i];
// parse the cigar if (idx[h.ctg] == null) continue;
var m, l_ins, n_ins, l_del, n_del, l_match, l_skip, l_clip; var a = idx[h.ctg](h.start, h.end);
l_ins = l_del = n_ins = n_del = l_match = l_skip = l_clip = 0;
while ((m = re_cigar.exec(h[4])) != 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;
}
h[3] = h[2] + l_match + l_del + l_skip;
h[5] = h[5] > l_del + l_ins? h[5] : l_del + l_ins;
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);
h.push(score);
if (idx[h[0]] == null) continue;
var a = idx[h[0]](h[2], h[3]);
if (a == null || a.length == 0) continue; if (a == null || a.length == 0) continue;
// find the approximate position on the primary assembly // find the approximate position on the primary assembly
var regs = []; var lifted = [];
for (var j = 0; j < a.length; ++j) { for (var j = 0; j < a.length; ++j) {
var s, e; var s, e;
if (!a[j][4]) { // ALT is mapped to the forward strand of the primary assembly if (!a[j][4]) { // ALT is mapped to the forward strand of the primary assembly
s = cigar2pos(a[j][6], h[2]); s = cigar2pos(a[j][6], h.start);
e = cigar2pos(a[j][6], h[3] - 1) + 1; e = cigar2pos(a[j][6], h.end - 1) + 1;
} else { } else {
s = cigar2pos(a[j][6], a[j][2] - h[3]); s = cigar2pos(a[j][6], a[j][2] - h.end);
e = cigar2pos(a[j][6], a[j][2] - h[2] - 1) + 1; 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 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]; s += a[j][5]; e += a[j][5];
//print("*", a[j][4], h[0], a[j][3], s, e); lifted.push([a[j][3], (h.rev!=a[j][4]), s, e]);
regs.push([a[j][3], (h[1]!=a[j][4]), s, e]);
} }
if (regs.length == 0) continue; if (lifted.length) ++n_lifted, hits[i].lifted = lifted;
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
++n_lifted;
} }
if (n_lifted == 0) { if (n_lifted == 0) {
//print(line); if (opt.verbose < 4) print(line);
continue; continue;
} }
// group hits // group hits
var phits = [];
for (var i = 0; i < hits.length; ++i) { for (var i = 0; i < hits.length; ++i) {
var h = hits[i]; if (hits[i].lifted && hits[i].lifted.length) // TODO: only the first element in lifted[] is used
if (h.length > 7) phits.push([h[7], h[9], h[10], -1, i]); // lifted 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 phits.push([h[0], h[2], h[3], -1, i]); 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
} }
phits.sort(function(a,b) { hits.sort(function(a,b) { return a.pctg != b.pctg? (a.pctg < b.pctg? -1 : 1) : a.pstart - b.pstart });
if (a[0] != b[0]) return a[0] < b[0]? -1 : 1; var last_chr = null, end = 0, g = -1;
if (a[1] != b[1]) return a[1] - b[1]; for (var i = 0; i < hits.length; ++i) {
}); if (last_chr != hits[i].pctg) ++g, last_chr = hits[i].pctg, end = 0;
var last_chr = null, end = 0, groupid = -1; else if (hits[i].pstart >= end) ++g;
for (var i = 0; i < phits.length; ++i) { hits[i].g = g;
if (last_chr != phits[i][0]) { // change of chr end = end > hits[i].pend? end : hits[i].pend;
phits[i][3] = ++groupid;
last_chr = phits[i][0], end = phits[i][2];
} else if (phits[i][1] >= end) { // no overlap
phits[i][3] = ++groupid;
end = phits[i][2];
} else {
phits[i][3] = groupid;
end = end > phits[i][2]? end : phits[i][2];
} }
} var reported_g = null, reported_i = null;
var reported_groupid = null; for (var i = 0; i < hits.length; ++i)
for (var i = 0; i < phits.length; ++i) if (hits[i].i == 0)
if (phits[i][4] == 0) reported_groupid = phits[i][3]; reported_g = hits[i].g, reported_i = i;
var n_group0 = 0; // #hits overlapping the reported hit var n_group0 = 0; // #hits overlapping the reported hit
for (var i = 0; i < phits.length; ++i) for (var i = 0; i < hits.length; ++i)
if (phits[i][3] == phits[reported_groupid][3]) if (hits[i].g == reported_g)
++n_group0; ++n_group0;
if (n_group0 == 1) { // then keep the reported alignment and mapQ if (n_group0 == 1) { // then keep the reported alignment and mapQ
//print(line); if (opt.verbose < 4) print(line);
continue; continue;
} }
// re-estimate mapQ // re-estimate mapQ
var group_max = []; var group_max = [];
for (var i = 0; i < phits.length; ++i) for (var i = 0; i < hits.length; ++i) {
if (group_max[phits[i][3]] == null || group_max[phits[i][3]][0] < hits[phits[i][4]][6]) var g = hits[i].g;
group_max[phits[i][3]] = [hits[phits[i][4]][6], phits[i][3]]; if (group_max[g] == null || group_max[g][0] < hits[i].score)
group_max[g] = [hits[i].score, g];
}
if (group_max.length > 1) if (group_max.length > 1)
group_max.sort(function(x,y) {return y[0]-x[0]}); group_max.sort(function(x,y) {return y[0]-x[0]});
var mapQ; var mapQ;
if (group_max[0][1] == reported_groupid) { // the best hit is the hit reported in SAM 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]); mapQ = group_max.length == 1? 60 : 6 * (group_max[0][0] - group_max[1][0]);
} else mapQ = 0; } else mapQ = 0;
mapQ = mapQ < 60? mapQ : 60; mapQ = mapQ < 60? mapQ : 60;
var ori_mapQ = parseInt(t[4]); var ori_mapQ = parseInt(t[4]);
mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ; mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ;
// print // generate lifted_str
t[4] = mapQ; for (var i = 0; i < hits.length; ++i) {
print(t.join("\t")); if (hits[i].lifted && hits[i].lifted.length) {
for (var i = 0; i < phits.length; ++i) { var lifted = hits[i].lifted;
var u = '';
for (var j = 0; j < lifted.length; ++j)
u += lifted[j][0] + "," + lifted[j][2] + "," + lifted[j][3] + "," + (lifted[j][1]?'-':'+') + ";";
hits[i].lifted_str = u;
}
}
// print
var rs = null, rq = null; // reversed quality and reverse complement sequence
t[4] = mapQ;
t.push("om:i:"+ori_mapQ);
if (hits[reported_i].lifted_str) t.push("lt:Z:" + hits[reported_i].lifted_str);
print(t.join("\t"));
var 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();
}
var cnt = 0;
for (var i = 0; i < hits.length; ++i) {
if (hits[i].g != reported_g || i == reported_i) continue;
//print(obj2str(hits[i]));
var s = [t[0], flag&0xf10, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0];
// update name
if (flag&0x40) s[0] += "/1";
if (flag&0x80) s[0] += "/2";
s[0] += "_" + (++cnt);
if (hits[i].rev == hits[reported_i].rev) s.push(t[9], t[10]);
else s.push(rs, rq);
s.push("NM:i:" + hits[i].NM);
if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);
print(s.join("\t"));
} }
print("*", mapQ, ori_mapQ);
for (var i = 0; i < hits.length; ++i)
print(hits[i]);
} }
file.close(); file.close();
aux.destroy();
buf.destroy(); buf.destroy();
} }
@ -588,7 +680,8 @@ function main(args)
{ {
if (args.length == 0) { if (args.length == 0) {
print("\nUsage: k8 bwa-helper.js <command> [arguments]\n"); print("\nUsage: k8 bwa-helper.js <command> [arguments]\n");
print("Commands: sam2pas convert SAM to pairwise alignment summary format (PAS)"); print("Commands: genalt generate ALT alignments");
print(" sam2pas convert SAM to pairwise alignment summary format (PAS)");
print(" pas2reg extract covered regions"); print(" pas2reg extract covered regions");
print(" reg2cut regions to extract for the 2nd round bwa-mem"); print(" reg2cut regions to extract for the 2nd round bwa-mem");
print(" markovlp identify bi-directional overlaps"); print(" markovlp identify bi-directional overlaps");