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code backup

This commit is contained in:
Heng Li 2014-10-02 23:48:03 -04:00
parent 7026b3ec68
commit 2c3619d569
1 changed files with 23 additions and 0 deletions
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23
bwa-postalt.js
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@ -401,6 +401,29 @@ function bwa_postalt(args)
else mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ; else mapQ = mapQ > ori_mapQ? mapQ : ori_mapQ;
} else mapQ = t[4]; } else mapQ = t[4];
// ALT genotyping
{
var hits2 = [];
for (var i = 0; i < hits.length; ++i) {
var h = hits[i];
if (h.g == reported_g)
hits2.push([h.pctg, h.pstart, h.pend, h.ctg, h.score]);
}
var start = hits2[0][1], end = hits2[0][2];
for (var i = 1; i < hits2.length; ++i)
end = end > hits2[i][2]? end : hits2[i][2];
var alts = {};
for (var i = 0; i < hits2.length; ++i)
if (idx_alt[hits2[i][3]] != null || idx_un[hits2[i][3]] != null)
alts[hits2[i][3]] = hits2[i][4];
if (idx_pri[hits2[0][0]] != null) {
var ovlp = idx_pri[hits2[0][0]](start, end);
for (var i = 0; i < ovlp.length; ++i)
if (alts[ovlp[i][2]] == null) alts[ovlp[i][2]] = 0;
}
print(obj2str(alts));
}
// check if the reported hit overlaps a hit to the primary assembly; if so, don't reduce mapping quality // 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) { if (opt.recover_mapq && n_rpt_lifted == 1 && mapQ > 0) {
var l = rpt_lifted; var l = rpt_lifted;