Imported Upstream version 0.5

[pysam.git] / samtools / bam_reheader.c

diff --git a/samtools/bam_reheader.c b/samtools/bam_reheader.c
deleted file mode 100644 (file)
index bae97c7..0000000
--- a/samtools/bam_reheader.c
+++ /dev/null
@@ -1,60 +0,0 @@
-#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)
-#else
-       while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
-#endif
-               fwrite(buf, 1, len, fp->x.fpw);
-       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(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;
-}