new file mode 100644

@@ -0,0 +1,64 @@

+#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 */