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keep RG

This commit is contained in:
Heng Li 2014-10-27 10:45:07 -04:00
parent dbe74ca9b8
commit 5c87869d91
1 changed files with 2 additions and 0 deletions
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2
bwa-postalt.js
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@ -577,6 +577,7 @@ function bwa_postalt(args)
// stage the hits generated from the XA tag
var cnt = 0;
var rg = (m = /\t(RG:Z:\S+)/.exec(line)) != null? m[1] : null;
for (var i = 0; i < hits.length; ++i) {
if (opt.verbose >= 5) print(obj2str(hits[i]));
if (hits[i].g != reported_g || i == reported_i) continue;
@ -592,6 +593,7 @@ function bwa_postalt(args)
}
s.push("NM:i:" + hits[i].NM);
if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);
if (rg != null) s.push(rg);
buf2.push(s);
}
}