X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_mate.c;h=61f808a26402e9bd1d332f40074b4b3ca1f89dd3;hb=1443ba19e5d810a30b7918f6213e3badc39597f0;hp=bb5360521adaa1cc8b785b3d7d0f1bbd58bae8fd;hpb=635998cfe030da5f3dbec42a6daa3ca82fa5c871;p=samtools.git

diff --git a/bam_mate.c b/bam_mate.c
index bb53605..61f808a 100644
--- a/bam_mate.c
+++ b/bam_mate.c
@@ -29,9 +29,9 @@ void bam_mating_core(bamFile in, bamFile out)
 					pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
 					cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
 				} else cur->core.isize = pre->core.isize = 0;
-				if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FREVERSE;
+				if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
 				else cur->core.flag &= ~BAM_FMREVERSE;
-				if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FREVERSE;
+				if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
 				else pre->core.flag &= ~BAM_FMREVERSE;
 				if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
 				if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
@@ -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;