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comparison pyPRADA_1.2/tools/samtools-0.1.16/bam_reheader.c @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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-1:000000000000 0:acc2ca1a3ba4
1 #include <stdio.h>
2 #include <stdlib.h>
3 #include "bgzf.h"
4 #include "bam.h"
5
6 #define BUF_SIZE 0x10000
7
8 int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
9 {
10 BGZF *fp;
11 bam_header_t *old;
12 int len;
13 uint8_t *buf;
14 if (in->open_mode != 'r') return -1;
15 buf = malloc(BUF_SIZE);
16 old = bam_header_read(in);
17 fp = bgzf_fdopen(fd, "w");
18 bam_header_write(fp, h);
19 if (in->block_offset < in->block_length) {
20 bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
21 bgzf_flush(fp);
22 }
23 #ifdef _USE_KNETFILE
24 while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
25 fwrite(buf, 1, len, fp->x.fpw);
26 #else
27 while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
28 fwrite(buf, 1, len, fp->file);
29 #endif
30 free(buf);
31 fp->block_offset = in->block_offset = 0;
32 bgzf_close(fp);
33 return 0;
34 }
35
36 int main_reheader(int argc, char *argv[])
37 {
38 bam_header_t *h;
39 BGZF *in;
40 if (argc != 3) {
41 fprintf(stderr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
42 return 1;
43 }
44 { // read the header
45 tamFile fph = sam_open(argv[1]);
46 if (fph == 0) {
47 fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
48 return 1;
49 }
50 h = sam_header_read(fph);
51 sam_close(fph);
52 }
53 in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
54 if (in == 0) {
55 fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[2]);
56 return 1;
57 }
58 bam_reheader(in, h, fileno(stdout));
59 bgzf_close(in);
60 return 0;
61 }