From: On behalf of John Marshall <lh3@sanger.ac.uk>
Date: Fri, 24 Sep 2010 15:08:24 +0000 (+0000)
Subject: Use bam_validate1() to detect garbage records in the event of a corrupt
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=ccd987169ea085165fe156e1727fbb9a33057f7b;p=samtools.git

Use bam_validate1() to detect garbage records in the event of a corrupt
BAI index file that causes a bam_seek() to an invalid position.  At most
one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
call, so the cost is insignificant in the normal case.
---

diff --git a/bam_index.c b/bam_index.c
index 263561b..1ad2e93 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -676,7 +676,10 @@ int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
 		}
 		if ((ret = bam_read1(fp, b)) >= 0) {
 			iter->curr_off = bam_tell(fp);
-			if (b->core.tid != iter->tid || b->core.pos >= iter->end) { ret = -1; break; } // no need to proceed
+			if (b->core.tid != iter->tid || b->core.pos >= iter->end) { // no need to proceed
+				ret = bam_validate1(NULL, b)? -1 : -5; // determine whether end of region or error
+				break;
+			}
 			else if (is_overlap(iter->beg, iter->end, b)) return ret;
 		} else break; // end of file or error
 	}