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bam_reheader.c

#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;
}

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