* samtools-0.1.5-17 (r422)

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 2edb2a8b1e339fb99ee3a9c085d1d61bd1881db2..52d97a6959dfad2076afdb3c64f37fd76b87fb40 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -91,7 +91,11 @@ bam_header_t *bam_header_read(bamFile fp)
 {
        bam_header_t *header;
        char buf[4];
-       int32_t i, name_len;
+       int32_t i = 1, name_len;
+       // check EOF
+       i = bgzf_check_EOF(fp);
+       if (i < 0) fprintf(stderr, "[bam_header_read] read from pipe; skip EOF checking.\n");
+       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)) {