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This commit is contained in:
Heng Li
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5fc0f44e27
commit
8d61316cc8
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@ -13,6 +13,7 @@
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*** From k8.js ***
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******************/
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// Parse command-line options. A BSD getopt() clone in javascript.
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var getopt = function(args, ostr) {
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var oli; // option letter list index
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if (typeof(getopt.place) == 'undefined')
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@ -51,6 +52,7 @@ var getopt = function(args, ostr) {
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return optopt;
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}
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// print an object in a format similar to JSON. For debugging.
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function obj2str(o)
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{
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if (typeof(o) != 'object') {
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@ -75,6 +77,7 @@ function obj2str(o)
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}
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}
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// reverse a string
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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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@ -84,6 +87,7 @@ Bytes.prototype.reverse = function()
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}
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}
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// reverse complement a DNA string
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Bytes.prototype.revcomp = function()
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{
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if (Bytes.rctab == null) {
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@ -103,13 +107,8 @@ Bytes.prototype.revcomp = function()
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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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*** Generate ALT alignment ***
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******************************/
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function intv_ovlp(intv, bits) // interval index
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// create index for a list of intervals for fast interval queries; ported from bedidx.c in samtools
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function intv_ovlp(intv, bits)
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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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@ -142,7 +141,14 @@ function intv_ovlp(intv, bits) // interval index
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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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var re_cigar = /(\d+)([MIDSHN])/g;
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/******************************
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*** Generate ALT alignment ***
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******************************/
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// given a pos on ALT and the ALT-to-REF CIGAR, find the pos on REF
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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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@ -166,7 +172,9 @@ function cigar2pos(cigar, pos) // given a pos on ALT and the ALT-to-REF CIGAR, f
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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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// Parse a hit. $s is an array that looks something like ["chr1", "+12345", "100M", 5]
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// Return an object keeping various information about the alignment.
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function parse_hit(s, opt)
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{
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var h = {};
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h.ctg = s[0];
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@ -221,7 +229,7 @@ function read_ALT_sam(fn)
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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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// create index for intervals on ALT contigs
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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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@ -270,20 +278,22 @@ function bwa_postalt(args)
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var t = line.split("\t");
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t[1] = parseInt(t[1]); t[3] = parseInt(t[3]); t[4] = parseInt(t[4]);
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if (buf2.length && buf2[0][0] != t[0]) {
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// print bufferred reads
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if (buf2.length && (buf2[0][0] != t[0] || (buf2[0][1]&0xc0) != (t[1]&0xc0))) {
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for (var i = 0; i < buf2.length; ++i)
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print(buf2[i].join("\t"));
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buf2 = [];
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}
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if ((m = /\tXA:Z:(\S+)/.exec(line)) == null) { // TODO: this does not work with PE file
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if ((m = /\tXA:Z:(\S+)/.exec(line)) == null) {
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buf2.push(t);
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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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// parse the reported hit
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var hits = [];
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var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
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var flag = t[1];
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var h = parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt);
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@ -292,11 +302,13 @@ function bwa_postalt(args)
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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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// parse hits in the XA tag
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for (var i = 0; i < XA_strs.length; ++i)
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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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// lift mapping positions to the primary assembly
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var n_lifted = 0, n_rpt_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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@ -328,7 +340,7 @@ function bwa_postalt(args)
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continue;
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}
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// group hits
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// group hits based on the lifted positions on the primary assembly
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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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@ -352,8 +364,9 @@ function bwa_postalt(args)
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if (hits[i].g == reported_g)
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++n_group0;
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// re-estimate mapping quality if necessary
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var mapQ, ori_mapQ = t[4];
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if (n_group0 > 1) { // then re-estimate mapQ
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if (n_group0 > 1) {
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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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@ -414,11 +427,13 @@ function bwa_postalt(args)
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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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// stage the reported hit
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t[4] = mapQ;
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if (n_group0 > 1) 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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buf2.push(t);
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// stage the hits generated from the XA tag
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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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