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comparison PsiCLASS-1.0.2/samtools-0.1.19/examples/calDepth.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 "sam.h"
3
4 typedef struct {
5 int beg, end;
6 samfile_t *in;
7 } tmpstruct_t;
8
9 // callback for bam_fetch()
10 static int fetch_func(const bam1_t *b, void *data)
11 {
12 bam_plbuf_t *buf = (bam_plbuf_t*)data;
13 bam_plbuf_push(b, buf);
14 return 0;
15 }
16 // callback for bam_plbuf_init()
17 static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
18 {
19 tmpstruct_t *tmp = (tmpstruct_t*)data;
20 if ((int)pos >= tmp->beg && (int)pos < tmp->end)
21 printf("%s\t%d\t%d\n", tmp->in->header->target_name[tid], pos + 1, n);
22 return 0;
23 }
24
25 int main(int argc, char *argv[])
26 {
27 tmpstruct_t tmp;
28 if (argc == 1) {
29 fprintf(stderr, "Usage: calDepth <in.bam> [region]\n");
30 return 1;
31 }
32 tmp.beg = 0; tmp.end = 0x7fffffff;
33 tmp.in = samopen(argv[1], "rb", 0);
34 if (tmp.in == 0) {
35 fprintf(stderr, "Fail to open BAM file %s\n", argv[1]);
36 return 1;
37 }
38 if (argc == 2) { // if a region is not specified
39 sampileup(tmp.in, -1, pileup_func, &tmp);
40 } else {
41 int ref;
42 bam_index_t *idx;
43 bam_plbuf_t *buf;
44 idx = bam_index_load(argv[1]); // load BAM index
45 if (idx == 0) {
46 fprintf(stderr, "BAM indexing file is not available.\n");
47 return 1;
48 }
49 bam_parse_region(tmp.in->header, argv[2], &ref, &tmp.beg, &tmp.end); // parse the region
50 if (ref < 0) {
51 fprintf(stderr, "Invalid region %s\n", argv[2]);
52 return 1;
53 }
54 buf = bam_plbuf_init(pileup_func, &tmp); // initialize pileup
55 bam_fetch(tmp.in->x.bam, idx, ref, tmp.beg, tmp.end, buf, fetch_func);
56 bam_plbuf_push(0, buf); // finalize pileup
57 bam_index_destroy(idx);
58 bam_plbuf_destroy(buf);
59 }
60 samclose(tmp.in);
61 return 0;
62 }