From: Heng Li <lh3@live.co.uk>
Date: Sat, 25 Apr 2009 10:49:40 +0000 (+0000)
Subject:  * samtools-0.1.3-6 (r244)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=99a3d0d13f7668b26ec6b47b100ee6232d49d336;p=samtools.git

 * samtools-0.1.3-6 (r244)
 * fixed segfault for unmapped reads
---

diff --git a/bam_md.c b/bam_md.c
index a7d2ab4..9abff46 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -70,7 +70,7 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
 
 int bam_fillmd(int argc, char *argv[])
 {
-	int c, is_equal = 0, tid = -1, ret, len;
+	int c, is_equal = 0, tid = -2, ret, len;
 	bamFile fp, fpout = 0;
 	bam_header_t *header;
 	faidx_t *fai;
@@ -96,12 +96,14 @@ int bam_fillmd(int argc, char *argv[])
 
 	b = bam_init1();
 	while ((ret = bam_read1(fp, b)) >= 0) {
-		if (tid != b->core.tid) {
-			free(ref);
-			ref = fai_fetch(fai, header->target_name[b->core.tid], &len);
-			tid = b->core.tid;
+		if (b->core.tid >= 0) {
+			if (tid != b->core.tid) {
+				free(ref);
+				ref = fai_fetch(fai, header->target_name[b->core.tid], &len);
+				tid = b->core.tid;
+			}
+			bam_fillmd1(b, ref, is_equal);
 		}
-		bam_fillmd1(b, ref, is_equal);
 		bam_write1(fpout, b);
 	}
 	bam_destroy1(b);
diff --git a/bamtk.c b/bamtk.c
index fa256ae..aed8a39 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-5 (r243)"
+#define PACKAGE_VERSION "0.1.3-6 (r244)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -160,7 +160,7 @@ static int usage()
 	fprintf(stderr, "         index       index alignment\n");
 	fprintf(stderr, "         fixmate     fix mate information\n");
 	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
-	fprintf(stderr, "         glfview     print GLFv2 file\n");
+	fprintf(stderr, "         glfview     print GLFv3 file\n");
 	fprintf(stderr, "         flagstat    simple stats\n");
 	fprintf(stderr, "         fillmd      fill the MD tag and change identical base to =\n");
 	fprintf(stderr, "\n");