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