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=0000000000000000000000000000000000000000;hp=35154d7172f60f4c5fb349b69c6853871f8dfc39;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=ca46ef4ba4a883c57cea62d5bf1bc021f1185109

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