zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

added postalt to bwa-helper for post processing

This commit is contained in:
Heng Li 2014-09-17 14:18:40 -04:00
parent 825ae92e58
commit f5a0e576e6
1 changed files with 156 additions and 67 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

141
bwa-helper.js
View File

@ -103,6 +103,8 @@ Bytes.prototype.revcomp = function()
this[this.length>>1] = Bytes.rctab[this[this.length>>1]]; this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
} }
var re_cigar = /(\d+)([MIDSHN])/g;
/************************ /************************
*** command markovlp *** *** command markovlp ***
************************/ ************************/
@ -432,12 +434,8 @@ function intv_ovlp(intv, bits) // interval index
} }
} }
function bwa_genalt(args) function cigar2pos(cigar, pos) // given a pos on ALT and the ALT-to-REF CIGAR, find the pos on REF
{ {
var re_cigar = /(\d+)([MIDSHN])/g;
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; var x = 0, y = 0;
for (var i = 0; i < cigar.length; ++i) { for (var i = 0; i < cigar.length; ++i) {
var op = cigar[i][0], len = cigar[i][1]; var op = cigar[i][0], len = cigar[i][1];
@ -458,10 +456,10 @@ function bwa_genalt(args)
} }
} }
return -1; return -1;
} }
function parse_hit(s, opt) // parse a hit. s looks something like ["chr1", "+12345", "100M", 5] function parse_hit(s, opt) // parse a hit. s looks something like ["chr1", "+12345", "100M", 5]
{ {
var h = {}; var h = {};
h.ctg = s[0]; h.ctg = s[0];
h.start = parseInt(s[1].substr(1)) - 1; h.start = parseInt(s[1].substr(1)) - 1;
@ -487,25 +485,14 @@ function bwa_genalt(args)
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.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; h.l_query = l_match + l_ins + l_clip;
return h; return h;
} }
var c, opt = { a:1, b:4, o:6, e:1, verbose:3 }; // read the ALT-to-REF alignment and generate the index
function read_ALT_sam(fn)
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]");
exit(1);
}
var file, buf = new Bytes();
var aux = new Bytes(); // used for reverse and reverse complement
// read the ALT-to-REF alignment and generate the index
var intv = {}; var intv = {};
file = new File(args[getopt.ind]); var file = new File(fn);
var buf = new Bytes();
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");
@ -524,11 +511,31 @@ function bwa_genalt(args)
intv[t[0]].push([start, start + l_qaln, l_qaln + l_qclip, t[2], flag&16? true : false, parseInt(t[3]) - 1, cigar]); 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); //print(start, start + l_qaln, t[2], flag&16? true : false, parseInt(t[3]), cigar);
} }
buf.destroy();
file.close(); file.close();
// create the interval index // create the interval index
var idx = {}; var idx = {};
for (var ctg in intv) for (var ctg in intv)
idx[ctg] = intv_ovlp(intv[ctg]); idx[ctg] = intv_ovlp(intv[ctg]);
return idx;
}
function bwa_genalt(args)
{
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]");
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]);
// process SAM // process SAM
file = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : new File(); file = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : new File();
@ -682,6 +689,86 @@ function bwa_genalt(args)
buf.destroy(); buf.destroy();
} }
// This is in effect a simplified version of bwa_genalt().
function bwa_postalt(args)
{
var c, idx = {}, opt = { verbose:3, min_pa:0.8 };
while ((c = getopt(args, 'v:r:a:')) != null) {
if (c == 'v') opt.verbose = parseInt(getopt.arg);
else if (c == 'r') opt.min_pa = parseFloat(getopt.arg);
else if (c == 'a') idx = read_ALT_sam(getopt.arg);
}
if (args.length == getopt.ind) {
print("Usage: k8 bwa-helper.js postalt [-r "+opt.min_pa+"] [-a alt.sam] [aln.sam]");
exit(1);
}
// process SAM
var file = args.length - getopt.ind >= 1? new File(args[getopt.ind]) : new File();
var buf = new Bytes();
while (file.readline(buf) >= 0) {
var m, line = buf.toString();
if (line.charAt(0) == '@') {
print(line);
continue;
}
var t = line.split("\t");
var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
var flag = parseInt(t[1]);
var h = parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt);
// lift mapping positions to coordinates on the primary assembly
{
var a = null;
if (idx[h.ctg] != null)
a = idx[h.ctg](h.start, h.end);
if (a == null) a = [];
// 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]);
}
h.lifted = lifted;
}
// update mapQ if necessary
var ori_mapQ = null;
if ((m = /\tpa:f:(\d+\.\d+)/.exec(line)) != null) {
if (parseFloat(m[1]) < opt.min_pa)
ori_mapQ = t[4], t[4] = 0;
}
// generate lifted_str
if (h.lifted && h.lifted.length) {
var lifted = h.lifted;
var u = '';
for (var j = 0; j < lifted.length; ++j)
u += lifted[j][0] + "," + lifted[j][2] + "," + lifted[j][3] + "," + (lifted[j][1]?'-':'+') + ";";
h.lifted_str = u;
} else h.lifted_str = null;
// print
if (ori_mapQ != null) t.push("om:i:"+ori_mapQ);
if (h.lifted_str) t.push("lt:Z:" + h.lifted_str);
print(t.join("\t"));
}
buf.destroy();
file.close();
}
/********************* /*********************
*** Main function *** *** Main function ***
*********************/ *********************/
@ -690,7 +777,8 @@ 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: genalt generate ALT alignments"); print("Commands: postalt post process ALT-aware alignments");
print(" genalt generate ALT alignments for ALT-unaware alignments");
print(" sam2pas convert SAM to pairwise alignment summary format (PAS)"); 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");
@ -708,6 +796,7 @@ function main(args)
else if (cmd == 'pas2reg') bwa_pas2reg(args); else if (cmd == 'pas2reg') bwa_pas2reg(args);
else if (cmd == 'reg2cut') bwa_reg2cut(args); else if (cmd == 'reg2cut') bwa_reg2cut(args);
else if (cmd == 'genalt') bwa_genalt(args); else if (cmd == 'genalt') bwa_genalt(args);
else if (cmd == 'postalt') bwa_postalt(args);
else if (cmd == 'shortname') bwa_shortname(args); else if (cmd == 'shortname') bwa_shortname(args);
else warn("Unrecognized command"); else warn("Unrecognized command");
} }