From: On behalf of John Marshall <lh3@sanger.ac.uk>
Date: Sat, 27 Feb 2010 11:48:17 +0000 (+0000)
Subject: Improve the invalid 'BAM\1' magic number error message, and also print it
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=ce728f5471254d2bf6aaa0fbdabcf7ff173f4655;p=samtools.git

Improve the invalid 'BAM\1' magic number error message, and also print it
when no bytes can be read from the alleged BAM file, e.g., in the common
user error case when a SAM file has accidentally been supplied.
---

diff --git a/bam.c b/bam.c
index 56c95db..35e5863 100644
--- a/bam.c
+++ b/bam.c
@@ -70,6 +70,7 @@ bam_header_t *bam_header_read(bamFile fp)
 {
 	bam_header_t *header;
 	char buf[4];
+	int magic_len;
 	int32_t i = 1, name_len;
 	// check EOF
 	i = bgzf_check_EOF(fp);
@@ -80,9 +81,9 @@ bam_header_t *bam_header_read(bamFile fp)
 	}
 	else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent.\n");
 	// read "BAM1"
-	if (bam_read(fp, buf, 4) != 4) return 0;
-	if (strncmp(buf, "BAM\001", 4)) {
-		fprintf(stderr, "[bam_header_read] wrong header\n");
+	magic_len = bam_read(fp, buf, 4);
+	if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
+		fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
 		return 0;
 	}
 	header = bam_header_init();