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mate chr is sometimes wrong

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Heng Li 2014-11-10 10:16:53 -05:00
parent b2b42cea7e
commit a81603217e
1 changed files with 1 additions and 0 deletions
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bwa-postalt.js
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@ -479,6 +479,7 @@ function bwa_postalt(args)
if (hits[i].g != reported_g || i == reported_i) continue;
if (idx_alt[hits[i].ctg] == null) continue;
var s = [t[0], 0, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, t[6], t[7], t[8]];
if (t[6] == '=' && s[2] != t[2]) s[6] = t[2];
// print sequence/quality and set the rev flag
if (hits[i].rev == hits[reported_i].rev) {
s.push(t[9], t[10]);