From: Heng Li <lh3@live.co.uk>
Date: Sat, 14 Feb 2009 21:22:30 +0000 (+0000)
Subject:  * samtools-0.1.2-7
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=1355b18da7f540a2a52d4512e32ba0ae9ef4845f

 * samtools-0.1.2-7
 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP
---

diff --git a/bam_mate.c b/bam_mate.c
index bb53605..f37f8f8 100644
--- 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;
diff --git a/bamtk.c b/bamtk.c
index 65b7d69..9521fdd 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-7"
+#define PACKAGE_VERSION "0.1.2-8"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);