From: Heng Li <lh3@live.co.uk>
Date: Thu, 2 Apr 2009 14:14:56 +0000 (+0000)
Subject:  * samtools-0.1.2-20
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;ds=sidebyside;h=5af1150d241e56b349f7d61fd228c67b475b3c19;p=samtools.git

 * samtools-0.1.2-20
 * check if file is truncated in flagstat
---

diff --git a/bam_stat.c b/bam_stat.c
index a4522da..b0cd301 100644
--- a/bam_stat.c
+++ b/bam_stat.c
@@ -33,13 +33,15 @@ bam_flagstat_t *bam_flagstat_core(bamFile fp)
 	bam_flagstat_t *s;
 	bam1_t *b;
 	bam1_core_t *c;
+	int ret;
 	s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
 	b = bam_init1();
 	c = &b->core;
-	while (bam_read1(fp, b) >= 0) {
+	while ((ret = bam_read1(fp, b)) >= 0)
 		flagstat_loop(s, c);
-	}
 	bam_destroy1(b);
+	if (ret != -1)
+		fprintf(stderr, "[bam_flagstat_core] Truncated file? Continue anyway.\n");
 	return s;
 }
 int bam_flagstat(int argc, char *argv[])
diff --git a/bamtk.c b/bamtk.c
index 792699e..aeb7d0a 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-19"
+#define PACKAGE_VERSION "0.1.2-20"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);