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