* samtools-0.1.2-7

[samtools.git] / bam_mate.c

diff --git a/bam_mate.c b/bam_mate.c
index bb5360521adaa1cc8b785b3d7d0f1bbd58bae8fd..f37f8f836b04b499cfeae8dc616e992bfe2c6310 100644 (file)
--- a/bam_mate.c
+++ b/bam_mate.c
@@ -40,8 +40,10 @@ void bam_mating_core(bamFile in, bamFile out)
                                has_prev = 0;
                        } else { // unpaired or singleton
                                pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
-                               pre->core.flag |= BAM_FMUNMAP;
-                               pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
+                               if (pre->core.flag & BAM_FPAIRED) {
+                                       pre->core.flag |= BAM_FMUNMAP;
+                                       pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
+                               }
                                bam_write1(out, pre);
                        }
                } else has_prev = 1;