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working largely as expected

This commit is contained in:
Heng Li 2014-10-21 00:16:41 -04:00
parent a6b5a30dab
commit 497913d404
1 changed files with 12 additions and 10 deletions
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8
bwa-postalt.js
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@ -205,7 +205,7 @@ function parse_hit(s, opt)
function bwa_postalt(args)
{
var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false, recover_mapq:true, min_mapq:10, min_sc:90, max_nm_sc:10, show_ev:false, min_pa_ratio:0.8 };
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:0.8 };
while ((c = getopt(args, 'Pqev:p:r:')) != null) {
if (c == 'v') opt.verbose = parseInt(getopt.arg);
@ -482,10 +482,11 @@ function bwa_postalt(args)
}
// check if the reported hit overlaps a hit to the primary assembly; if so, don't reduce mapping quality
if (opt.recover_mapq && n_rpt_lifted == 1 && mapQ > 0) {
var l = rpt_lifted;
if (opt.update_mapq && mapQ > 0 && n_rpt_lifted <= 1) {
var l = n_rpt_lifted == 1? rpt_lifted : null;
for (var i = 0; i < buf2.length; ++i) {
var s = buf2[i], is_ovlp = true;
if (l != null) {
if (l[0] != s[2]) is_ovlp = false; // different chr
if (((s[1]&16) != 0) != l[1]) is_ovlp = false; // different strand
var start = s[3] - 1, end = start;
@ -493,6 +494,7 @@ function bwa_postalt(args)
if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N')
end += parseInt(m[1]);
if (!(start < l[3] && l[2] < end)) is_ovlp = false; // no overlap
} else is_ovlp = false;
var om = -1, pa = 10.;
for (var j = 11; j < s.length; ++j)
if ((m = /^om:i:(\d+)/.exec(s[j])) != null)