Merge commit 'upstream/0.1.7a.dfsg'

[samtools.git] / bam_stat.c

diff --git a/bam_stat.c b/bam_stat.c
index c1c4a432ce8167448f31577d2ce0f650610ff626..ea9deee9d712c71bfd51f7574a5cae055a2c2ace 100644 (file)
--- 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) {                                                    \