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wrong flag in the SAM output

This commit is contained in:
Heng Li 2014-10-14 16:57:57 -04:00
parent c79427a22d
commit 647b0e828a
1 changed files with 2 additions and 2 deletions
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4
bwa-postalt.js
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@ -541,10 +541,10 @@ function bwa_postalt(args)
// print sequence/quality and set the rev flag // print sequence/quality and set the rev flag
if (hits[i].rev == hits[reported_i].rev) { if (hits[i].rev == hits[reported_i].rev) {
s.push(t[9], t[10]); s.push(t[9], t[10]);
s[1] = (flag & 0x10) | 0x800; s[1] = flag | 0x800;
} else { } else {
s.push(rs, rq); s.push(rs, rq);
s[1] = ((flag & 0x10) ^ 0x10) | 0x800; s[1] = (flag ^ 0x10) | 0x800;
} }
s.push("NM:i:" + hits[i].NM); s.push("NM:i:" + hits[i].NM);
if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str); if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);