From c0093264de2e8979f5b98318c57ae567ba3db0bf Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 22 Feb 2013 12:34:46 -0500
Subject: [PATCH] wrong logic: paired mapQ should <q_pe

---
 bwamem_pair.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bwamem_pair.c b/bwamem_pair.c
index 9fa3505..5dd5927 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -269,7 +269,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 		if (q_pe > 60) q_pe = 60;
 		// the following assumes no split hits
 		if (z[0] == 0 && z[1] == 0) { // the best hit 
-			q_pe = q_pe > q_se[0] + q_se[1]? q_pe : q_se[0] + q_se[1];
+			q_pe = q_pe < q_se[0] + q_se[1]? q_pe : q_se[0] + q_se[1];
 			if (q_pe > 60) q_pe = 60;
 			q_se[0] = is_tandem[0]? q_se[0] : q_pe;
 			q_se[1] = is_tandem[1]? q_se[1] : q_pe;