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comparison PsiCLASS-1.0.2/samtools-0.1.19/bam_reheader.c @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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-1:000000000000 0:903fc43d6227
1 #include <stdio.h>
2 #include <stdlib.h>
3 #include "knetfile.h"
4 #include "bgzf.h"
5 #include "bam.h"
6
7 #define BUF_SIZE 0x10000
8
9 int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
10 {
11 BGZF *fp;
12 bam_header_t *old;
13 int len;
14 uint8_t *buf;
15 if (in->is_write) return -1;
16 buf = malloc(BUF_SIZE);
17 old = bam_header_read(in);
18 fp = bgzf_fdopen(fd, "w");
19 bam_header_write(fp, h);
20 if (in->block_offset < in->block_length) {
21 bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
22 bgzf_flush(fp);
23 }
24 #ifdef _USE_KNETFILE
25 while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0)
26 fwrite(buf, 1, len, fp->fp);
27 #else
28 while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
29 fwrite(buf, 1, len, fp->file);
30 #endif
31 free(buf);
32 fp->block_offset = in->block_offset = 0;
33 bgzf_close(fp);
34 return 0;
35 }
36
37 int main_reheader(int argc, char *argv[])
38 {
39 bam_header_t *h;
40 BGZF *in;
41 if (argc != 3) {
42 fprintf(stderr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
43 return 1;
44 }
45 { // read the header
46 tamFile fph = sam_open(argv[1]);
47 if (fph == 0) {
48 fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
49 return 1;
50 }
51 h = sam_header_read(fph);
52 sam_close(fph);
53 }
54 in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
55 if (in == 0) {
56 fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[2]);
57 return 1;
58 }
59 bam_reheader(in, h, fileno(stdout));
60 bgzf_close(in);
61 return 0;
62 }