X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_reheader.c.pysam.c;fp=samtools%2Fbam_reheader.c.pysam.c;h=35154d7172f60f4c5fb349b69c6853871f8dfc39;hp=0000000000000000000000000000000000000000;hb=8ab946e230447a6fe686edabc5e3cfa445da1721;hpb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991

diff --git a/samtools/bam_reheader.c.pysam.c b/samtools/bam_reheader.c.pysam.c
new file mode 100644
index 0000000..35154d7
--- /dev/null
+++ b/samtools/bam_reheader.c.pysam.c
@@ -0,0 +1,63 @@
+#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;
+}