From e746a3eac7f11f548919e9d42e6b8c980fd0d68b Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 24 Dec 2014 13:22:46 -0500
Subject: [PATCH] r1038: wrong 0x100|0x800 flags in PE mode

---
 bwamem_pair.c | 6 ++++--
 main.c        | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/bwamem_pair.c b/bwamem_pair.c
index a85c28a..7950736 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -338,8 +338,10 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 			h[i].XA = XA[i]? XA[i][z[i]] : 0;
 			aa[i][n_aa[i]++] = h[i];
 			if (n_pri[i] < a[i].n) { // the read has ALT hits
-				g[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[n_pri[i]]);
-				g[i].flag |= 0x40<<i | extra_flag;
+				mem_alnreg_t *p = &a[i].a[n_pri[i]];
+				if (p->score < opt->T || p->secondary >= 0 || !p->is_alt) continue;
+				g[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, p);
+				g[i].flag |= 0x800 | 0x40<<i | extra_flag;
 				g[i].XA = XA[i]? XA[i][n_pri[i]] : 0;
 				aa[i][n_aa[i]++] = g[i];
 			}
diff --git a/main.c b/main.c
index 7a41b65..c29dc6b 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.11-r1037-dirty"
+#define PACKAGE_VERSION "0.7.11-r1038-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);