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keep mate positions

This commit is contained in:
Heng Li 2014-10-28 13:03:33 -04:00
parent 5c87869d91
commit 6f39715e6e
1 changed files with 1 additions and 1 deletions
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bwa-postalt.js
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@ -582,7 +582,7 @@ function bwa_postalt(args)
if (opt.verbose >= 5) print(obj2str(hits[i]));
if (hits[i].g != reported_g || i == reported_i) continue;
if (!opt.show_pri && idx_alt[hits[i].ctg] == null) continue;
var s = [t[0], 0, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0];
var s = [t[0], 0, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, t[6], t[7], t[8]];
// print sequence/quality and set the rev flag
if (hits[i].rev == hits[reported_i].rev) {
s.push(t[9], t[10]);