#include <stdio.h>

#include <stdlib.h>

#include "knetfile.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_dopen(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->fp, buf, BUF_SIZE)) > 0)

fwrite(buf, 1, len, fp->fp);

#else

while (!feof(in->fp) && (len = fread(buf, 1, BUF_SIZE, in->fp)) > 0)

fwrite(buf, 1, len, fp->fp);

#endif

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;

}