Imported Upstream version 0.1.8

[samtools.git] / bam_reheader.c

diff --git a/bam_reheader.c b/bam_reheader.c
new file mode 100644 (file)
index 0000000..bae97c7
--- /dev/null
+++ b/bam_reheader.c
@@ -0,0 +1,60 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include "bgzf.h"
+#include "bam.h"
+
+#define BUF_SIZE 0x10000
+
+int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
+{
+       BGZF *fp;
+       bam_header_t *old;
+       int len;
+       uint8_t *buf;
+       if (in->open_mode != 'r') return -1;
+       buf = malloc(BUF_SIZE);
+       old = bam_header_read(in);
+       fp = bgzf_fdopen(fd, "w");
+       bam_header_write(fp, h);
+       if (in->block_offset < in->block_length) {
+               bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
+               bgzf_flush(fp);
+       }
+#ifdef _USE_KNETFILE
+       while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
+#else
+       while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
+#endif
+               fwrite(buf, 1, len, fp->x.fpw);
+       free(buf);
+       fp->block_offset = in->block_offset = 0;
+       bgzf_close(fp);
+       return 0;
+}
+
+int main_reheader(int argc, char *argv[])
+{
+       bam_header_t *h;
+       BGZF *in;
+       if (argc != 3) {
+               fprintf(stderr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
+               return 1;
+       }
+       { // read the header
+               tamFile fph = sam_open(argv[1]);
+               if (fph == 0) {
+                       fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
+                       return 1;
+               }
+               h = sam_header_read(fph);
+               sam_close(fph);
+       }
+       in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
+       if (in == 0) {
+               fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[2]);
+               return 1;
+       }
+       bam_reheader(in, h, fileno(stdout));
+       bgzf_close(in);
+       return 0;
+}