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save reads mapped to each HLA gene 

for downstream typing
This commit is contained in:
Heng Li 2014-10-24 16:54:48 -04:00
parent ba3ab0ca98
commit 33938e1ed0
1 changed files with 36 additions and 5 deletions
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41
bwa-postalt.js
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@ -203,6 +203,24 @@ function parse_hit(s, opt)
return h;
}
function print_buffer(buf2, fp_hla)
{
var m, hla = {};
if (buf2.length == 0) return;
for (var i = 0; i < buf2.length; ++i) {
print(buf2[i].join("\t"));
if ((m = /^(HLA-[^\s\*]+)\*\d+/.exec(buf2[i][2])) != null)
hla[m[1]] = true;
}
if (fp_hla != null) {
var name = buf2[0][0] + '/' + (buf2[0][1]>>6&3) + ((buf2[0][1]&16)? '-' : '+');
for (var x in hla) {
if (fp_hla[x] != null);
fp_hla[x].write('@' + name + '\n' + buf2[0][9] + '\n+\n' + buf2[0][10] + '\n');
}
}
}
function bwa_postalt(args)
{
var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false, update_mapq:true, min_mapq:10, min_sc:90, max_nm_sc:10, show_ev:false, min_pa_ratio:1 };
@ -247,7 +265,7 @@ function bwa_postalt(args)
var buf = new Bytes();
// read ALT-to-REF alignment
var intv_alt = {}, intv_pri = {}, idx_un = {};
var intv_alt = {}, intv_pri = {}, idx_un = {}, hla_ctg = {};
var file = new File(args[getopt.ind]);
while (file.readline(buf) >= 0) {
var line = buf.toString();
@ -261,6 +279,10 @@ function bwa_postalt(args)
continue;
}
var m, cigar = [], l_qaln = 0, l_tlen = 0, l_qclip = 0;
if ((m = /^(HLA-[^\s\*]+)\*\d+/.exec(t[0])) != null) { // read HLA contigs
if (hla_ctg[m[1]] == null) hla_ctg[m[1]] = 0;
++hla_ctg[m[1]];
}
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
@ -283,6 +305,14 @@ function bwa_postalt(args)
for (var ctg in intv_pri)
idx_pri[ctg] = intv_ovlp(intv_pri[ctg]);
// initialize the list of HLA contigs
var fp_hla = null;
if (opt.pre) {
fp_hla = {};
for (var h in hla_ctg)
fp_hla[h] = new File(opt.pre + '.' + h + '.fq', "w");
}
// initialize the list of ALT contigs
var weight_alt = [];
for (var ctg in idx_alt)
@ -305,8 +335,7 @@ function bwa_postalt(args)
// print bufferred reads
if (buf2.length && (buf2[0][0] != t[0] || (buf2[0][1]&0xc0) != (t[1]&0xc0))) {
for (var i = 0; i < buf2.length; ++i)
print(buf2[i].join("\t"));
print_buffer(buf2, fp_hla);
buf2 = [];
}
@ -562,10 +591,12 @@ function bwa_postalt(args)
buf2.push(s);
}
}
for (var i = 0; i < buf2.length; ++i)
print(buf2[i].join("\t"));
print_buffer(buf2, fp_hla);
file.close();
if (fp_evi != null) fp_evi.close();
if (fp_hla != null)
for (var h in fp_hla)
fp_hla[h].close();
buf.destroy();
aux.destroy();