From 647b0e828a1297c2559c25c12cb948ca0a2481bb Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 14 Oct 2014 16:57:57 -0400
Subject: [PATCH] wrong flag in the SAM output

---
 bwa-postalt.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bwa-postalt.js b/bwa-postalt.js
index d4d959e..411cfdd 100644
--- a/bwa-postalt.js
+++ b/bwa-postalt.js
@@ -541,10 +541,10 @@ function bwa_postalt(args)
 			// print sequence/quality and set the rev flag
 			if (hits[i].rev == hits[reported_i].rev) {
 				s.push(t[9], t[10]);
-				s[1] = (flag & 0x10) | 0x800;
+				s[1] = flag | 0x800;
 			} else {
 				s.push(rs, rq);
-				s[1] = ((flag & 0x10) ^ 0x10) | 0x800;
+				s[1] = (flag ^ 0x10) | 0x800;
 			}
 			s.push("NM:i:" + hits[i].NM);
 			if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);