Suppress bgzf_check_EOF() messages when reading from a pipe, as there is

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 619b46a6718a773aa073e7ecede13ef5cd10dee8..f6e05ff4285ef6743387e33942b91c91bf0e85fc 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -1,5 +1,6 @@
 #include <stdio.h>
 #include <ctype.h>
+#include <errno.h>
 #include <assert.h>
 #include "bam.h"
 #include "bam_endian.h"
@@ -94,7 +95,11 @@ bam_header_t *bam_header_read(bamFile fp)
        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");
+       if (i < 0) {
+               // If the file is a pipe, checking the EOF marker will *always* fail
+               // with ESPIPE.  Suppress the error message in this case.
+               if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
+       }
        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;