src/samtools/bam_reheader.c
5bb21ad5
 #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->is_write) 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->fp, buf, BUF_SIZE)) > 0)
 		fwrite(buf, 1, len, fp->fp);
 #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;
 }
 
 #ifdef _MAIN                    /* Rsamtools */
 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;
 }
 #endif  /* Rsamtools */