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Merge commit 'upstream/0.1.15'
[samtools.git]
/
bam.c
diff --git
a/bam.c
b/bam.c
index 521c1dda7897aa2b4489b103e1ee1a84129d6c63..a65aed5d551053a50952e95d58a763a77fadd06e 100644
(file)
--- a/
bam.c
+++ b/
bam.c
@@
-7,7
+7,7
@@
#include "kstring.h"
#include "sam_header.h"
#include "kstring.h"
#include "sam_header.h"
-int bam_is_be = 0;
+int bam_is_be = 0
, bam_verbose = 2
;
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
/**************************
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
/**************************
@@
-79,7
+79,7
@@
bam_header_t *bam_header_read(bamFile fp)
// with ESPIPE. Suppress the error message in this case.
if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
}
// 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");
+ else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent.
The input is probably truncated.
\n");
// read "BAM1"
magic_len = bam_read(fp, buf, 4);
if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
// read "BAM1"
magic_len = bam_read(fp, buf, 4);
if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {