+++ /dev/null
-#include "pysam.h"
-
-#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)
- fwrite(buf, 1, len, fp->x.fpw);
-#else
- while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
- fwrite(buf, 1, len, fp->file);
-#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(pysamerr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
- return 1;
- }
- { // read the header
- tamFile fph = sam_open(argv[1]);
- if (fph == 0) {
- fprintf(pysamerr, "[%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(pysamerr, "[%s] fail to open file %s.\n", __func__, argv[2]);
- return 1;
- }
- bam_reheader(in, h, fileno(stdout));
- bgzf_close(in);
- return 0;
-}