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code backup

This commit is contained in:
Heng Li 2014-10-02 21:49:29 -04:00
parent cd44ac48cd
commit 7026b3ec68
1 changed files with 42 additions and 44 deletions
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86
bwa-postalt.js
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@ -203,44 +203,6 @@ function parse_hit(s, opt)
return h;
}
// read the ALT-to-REF alignment and generate the index
function read_ALT_sam(fn)
{
var intv_alt = {}, idx_un = {};
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 pos = parseInt(t[3]) - 1;
var flag = parseInt(t[1]);
if ((flag&4) || t[2] == '*') {
idx_un[t[0]] = true;
continue;
}
var m, cigar = [], l_qaln = 0, l_tlen = 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, l_tlen += l;
else if (m[2] == 'S' || m[2] == 'H') l_qclip += l;
else if (m[2] == 'D' || m[2] == 'N') l_tlen += l;
}
var j = flag&16? cigar.length-1 : 0;
var start = cigar[j][0] == 'S'? cigar[j][1] : 0;
if (intv_alt[t[0]] == null) intv_alt[t[0]] = [];
intv_alt[t[0]].push([start, start + l_qaln, l_qaln + l_qclip, t[2], flag&16? true : false, parseInt(t[3]) - 1, cigar]);
}
buf.destroy();
file.close();
// create index for intervals on ALT contigs
var idx_alt = {};
for (var ctg in intv_alt)
idx_alt[ctg] = intv_ovlp(intv_alt[ctg]);
return [idx_alt, idx_un];
}
function bwa_postalt(args)
{
var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false, recover_mapq:true };
@ -267,13 +229,46 @@ function bwa_postalt(args)
exit(1);
}
var file, buf = new Bytes();
var aux = new Bytes(); // used for reverse and reverse complement
var idx_pair = read_ALT_sam(args[getopt.ind]);
var idx_alt = idx_pair[0], idx_un = idx_pair[1];
var buf2 = [];
var buf = new Bytes();
// read ALT-to-REF alignment
var intv_alt = {}, intv_pri = {}, idx_un = {};
var file = new File(args[getopt.ind]);
while (file.readline(buf) >= 0) {
var line = buf.toString();
var t = line.split("\t");
if (line.charAt(0) == '@') continue;
var pos = parseInt(t[3]) - 1;
var flag = parseInt(t[1]);
if ((flag&4) || t[2] == '*') {
idx_un[t[0]] = true;
continue;
}
var m, cigar = [], l_qaln = 0, l_tlen = 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, l_tlen += l;
else if (m[2] == 'S' || m[2] == 'H') l_qclip += l;
else if (m[2] == 'D' || m[2] == 'N') l_tlen += l;
}
var j = flag&16? cigar.length-1 : 0;
var start = cigar[j][0] == 'S'? cigar[j][1] : 0;
if (intv_alt[t[0]] == null) intv_alt[t[0]] = [];
intv_alt[t[0]].push([start, start + l_qaln, l_qaln + l_qclip, t[2], flag&16? true : false, parseInt(t[3]) - 1, cigar]);
if (intv_pri[t[2]] == null) intv_pri[t[2]] = [];
intv_pri[t[2]].push([pos, pos + l_tlen, t[0]]);
}
file.close();
var idx_alt = {}, idx_pri = {};
for (var ctg in intv_alt)
idx_alt[ctg] = intv_ovlp(intv_alt[ctg]);
for (var ctg in intv_pri)
idx_pri[ctg] = intv_ovlp(intv_pri[ctg]);
// process SAM
var buf2 = [];
file = args.length - getopt.ind >= 2? new File(args[getopt.ind+1]) : new File();
while (file.readline(buf) >= 0) {
var m, line = buf.toString();
@ -323,7 +318,10 @@ function bwa_postalt(args)
has_alt = true;
break;
}
if (!has_alt) continue;
if (!has_alt) {
buf2.push(t);
continue;
}
// lift mapping positions to the primary assembly
var n_rpt_lifted = 0, rpt_lifted = null;
@ -479,8 +477,8 @@ function bwa_postalt(args)
print(buf2[i].join("\t"));
file.close();
aux.destroy();
buf.destroy();
aux.destroy();
}
bwa_postalt(arguments);