From: Heng Li <lh3@live.co.uk>
Date: Wed, 15 Apr 2009 12:00:08 +0000 (+0000)
Subject:  * samtools-0.1.2-26
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5fb80400b8e7ed3d7f782ad13897d6fcac2e03f1;p=samtools.git

 * samtools-0.1.2-26
 * fixed a bug in rmdup when there are unmapped reads
---

diff --git a/bam_rmdup.c b/bam_rmdup.c
index 321938f..5026901 100644
--- a/bam_rmdup.c
+++ b/bam_rmdup.c
@@ -76,6 +76,11 @@ void bam_rmdup_core(bamFile in, bamFile out)
 					fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
 					clear_del_set(del_set);
 				}
+				if ((int)c->tid == -1) { // append unmapped reads
+					bam_write1(out, b);
+					while (bam_read1(in, b) >= 0) bam_write1(out, b);
+					break;
+				}
 				last_tid = c->tid;
 				fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", header->target_name[c->tid]);
 			}
diff --git a/bamtk.c b/bamtk.c
index 096cb90..e0bccb7 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-25"
+#define PACKAGE_VERSION "0.1.2-26"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);