From: Heng Li <lh3@live.co.uk>
Date: Tue, 3 Feb 2009 10:43:11 +0000 (+0000)
Subject: fixed a potential memory problem in indexing
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=47c65ef17d8949832a0c79c552118b31154bc2ad;hp=69b7f0f3ffd72fac57642fccc8c61aae2fd2ce36;p=samtools.git

fixed a potential memory problem in indexing
---

diff --git a/bam_index.c b/bam_index.c
index 6bc735e..8c25552 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -158,7 +158,7 @@ bam_index_t *bam_index_core(bamFile fp)
 			fprintf(stderr, "[bam_index_core] the alignment is not sorted. Abort!\n");
 			exit(1);
 		}
-		if (b->core.bin < 4681) insert_offset2(&idx->index2[b->core.tid], b, last_off);
+		if (b->core.tid >= 0 && b->core.bin < 4681) insert_offset2(&idx->index2[b->core.tid], b, last_off);
 		if (c->bin != last_bin) { // then possibly write the binning index
 			if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
 				insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
diff --git a/bamtk.c b/bamtk.c
index 631502c..9b75ed6 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-3"
+#define PACKAGE_VERSION "0.1.2-4"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);