From 4fad92de778543eba158108f7b6885c672eda027 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Wed, 5 Aug 2009 09:44:24 +0000
Subject: [PATCH]  * samtools-0.1.5-25 (r436)  * in flagstats, do not report
 singletons if both ends are unmapped

---
 bam_stat.c | 2 +-
 bamtk.c    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bam_stat.c b/bam_stat.c
index c1c4a43..ea9deee 100644
--- a/bam_stat.c
+++ b/bam_stat.c
@@ -16,7 +16,7 @@ typedef struct {
 			if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good;		\
 			if ((c)->flag & BAM_FREAD1) ++(s)->n_read1;					\
 			if ((c)->flag & BAM_FREAD2) ++(s)->n_read2;					\
-			if ((c)->flag & BAM_FMUNMAP) ++(s)->n_sgltn;				\
+			if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn;	\
 			if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
 				++(s)->n_pair_map;										\
 				if ((c)->mtid != (c)->tid) {							\
diff --git a/bamtk.c b/bamtk.c
index 0b41561..08d0fdc 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-24 (r435)"
+#define PACKAGE_VERSION "0.1.5-25 (r436)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
-- 
2.39.5