* samtools-0.1.7-7 (r584)

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 56c95db4e2c42c404627e41bd1ca2360a496af73..86cf3f3b71f4ecedbb8e80a2033c664cd7ae3b27 100644 (file)
--- 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();
@@ -140,6 +141,7 @@ int bam_header_write(bamFile fp, const bam_header_t *header)
                        bam_write(fp, &x, 4);
                } else bam_write(fp, &header->target_len[i], 4);
        }
+       bgzf_flush(fp);
        return 0;
 }
 
@@ -207,6 +209,7 @@ inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8
        x[5] = c->mtid;
        x[6] = c->mpos;
        x[7] = c->isize;
+       bgzf_flush_try(fp, 4 + block_len);
        if (bam_is_be) {
                for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
                y = block_len;