From 7eabcf42c4ef102c25b71b20919463ed9767d363 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 10 Nov 2014 13:15:11 -0500
Subject: [PATCH] r983: bugfix - wrong mate info

Picard now gives a clean bill.
---
 bwamem_pair.c | 9 +++++++--
 main.c        | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/bwamem_pair.c b/bwamem_pair.c
index e405423..f8b5d46 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -362,8 +362,13 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
 
 no_pairing:
 	for (i = 0; i < 2; ++i) {
-		if (a[i].n && a[i].a[0].score >= opt->T)
-			h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[0]);
+		int which = -1;
+		if (a[i].n) {
+			if (a[i].a[0].score >= opt->T) which = 0;
+			else if (n_pri[i] < a[i].n && a[i].a[n_pri[i]].score >= opt->T)
+				which = n_pri[i];
+		}
+		if (which >= 0) h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[which]);
 		else h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, 0);
 	}
 	if (!(opt->flag & MEM_F_NOPAIRING) && h[0].rid == h[1].rid && h[0].rid >= 0) { // if the top hits from the two ends constitute a proper pair, flag it.
diff --git a/main.c b/main.c
index a69ffeb..f5448d7 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r963-dirty"
+#define PACKAGE_VERSION "0.7.10-r983-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);