X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_stat.c;h=ea9deee9d712c71bfd51f7574a5cae055a2c2ace;hb=fe9d679264cafa551db00fe309eea2858a536ee8;hp=81b7b6356ed2f32c255ddcf6129c38d84ca4ab15;hpb=56aa6ae865756f6e1ab5cf07b9f0548ad84f843f;p=samtools.git

diff --git a/bam_stat.c b/bam_stat.c
index 81b7b63..ea9deee 100644
--- a/bam_stat.c
+++ b/bam_stat.c
@@ -1,4 +1,5 @@
 #include <unistd.h>
+#include <assert.h>
 #include "bam.h"
 
 typedef struct {
@@ -15,7 +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) {							\