X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam_view.c;fp=sam_view.c;h=41b651abbacd0aa69d04f94299b9b79680642d08;hb=ca535cf5321de0a93406b8534f6bc03d01fb5644;hp=3b10e2e5372e98a2b9ebda4bd5791dc1b837a20f;hpb=8ad43dd70c21cfdd6a965a528363511b52d25c5f;p=samtools.git

diff --git a/sam_view.c b/sam_view.c
index 3b10e2e..41b651a 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -164,7 +164,12 @@ int main_samview(int argc, char *argv[])
 				fprintf(stderr, "[main_samview] fail to get the reference name. Continue anyway.\n");
 				continue;
 			}
-			bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); // fetch alignments
+			// fetch alignments
+			if (bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func) < 0) {
+				fprintf(stderr, "[main_samview] retrieval failed due to truncated file or corrupt BAM index file\n");
+				ret = 1;
+				break;
+			}
 		}
 		bam_index_destroy(idx); // destroy the BAM index
 	}