From 7144a0cefce0da81fea16b2e64a3ca285b78731e Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 9 Sep 2013 17:51:05 -0400
Subject: [PATCH] r415: bug in the new (optional) mapQ computation

I may use the new method as the default. Testing needed.
---
 bwamem.c | 2 +-
 main.c   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bwamem.c b/bwamem.c
index 6cc4639..293dd55 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -807,7 +807,7 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
 	} else if (opt->mapQ_coef_len > 0) {
 		double tmp;
 		tmp = l < opt->mapQ_coef_len? 1. : opt->mapQ_coef_fac / log(l);
-		tmp *= a->seedcov < l? (double)a->seedcov / identity : 1;
+		tmp *= identity * identity;
 		mapq = (int)(6.02 * (a->score - sub) / opt->a * tmp * tmp + .499);
 	} else {
 		mapq = (int)(MEM_MAPQ_COEF * (1. - (double)sub / a->score) * log(a->seedcov) + .499);
diff --git a/main.c b/main.c
index d1e3895..998719f 100644
--- a/main.c
+++ b/main.c
@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.5a-r414"
+#define PACKAGE_VERSION "0.7.5a-r415"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);