From 340babdd671eeeb3c7bfbf2e4ad1e761ece94983 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 11 Sep 2017 09:58:41 -0400
Subject: [PATCH] r1185: don't lower supp mapq with -5

---
 bwamem.c | 3 ++-
 main.c   | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index d7c00fe..a4e9068 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -1026,7 +1026,8 @@ void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
 		if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
 		if (l && p->secondary < 0) // if supplementary
 			q->flag |= (opt->flag&MEM_F_NO_MULTI)? 0x10000 : 0x800;
-		if (l && !p->is_alt && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
+		if (!(opt->flag&MEM_F_PRIMARY5) && l && !p->is_alt && q->mapq > aa.a[0].mapq)
+			q->mapq = aa.a[0].mapq; // lower mapq for supplementary mappings, unless -5 is applied
 		++l;
 	}
 	if (aa.n == 0) { // no alignments good enough; then write an unaligned record
diff --git a/main.c b/main.c
index e2b7cf1..189e723 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.16a-r1181"
+#define PACKAGE_VERSION "0.7.16a-r1185-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);