1 /* This program demonstrates how to generate pileup from multiple BAMs
2 * simutaneously, to achieve random access and to use the BED interface.
3 * To compile this program separately, you may:
5 * gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -L. -lbam -lz
13 typedef struct { // auxiliary data structure
14 bamFile fp; // the file handler
15 bam_iter_t iter; // NULL if a region not specified
16 int min_mapQ, min_len; // mapQ filter; length filter
19 void *bed_read(const char *fn); // read a BED or position list file
20 void bed_destroy(void *_h); // destroy the BED data structure
21 int bed_overlap(const void *_h, const char *chr, int beg, int end); // test if chr:beg-end overlaps
23 // This function reads a BAM alignment from one BAM file.
24 static int read_bam(void *data, bam1_t *b) // read level filters better go here to avoid pileup
26 aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
27 int ret = aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
28 if (!(b->core.flag&BAM_FUNMAP)) {
29 if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
30 else if (aux->min_len && bam_cigar2qlen(&b->core, bam1_cigar(b)) < aux->min_len) b->core.flag |= BAM_FUNMAP;
35 #ifdef _MAIN_BAM2DEPTH
36 int main(int argc, char *argv[])
38 int main_depth(int argc, char *argv[])
41 int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0;
42 const bam_pileup1_t **plp;
43 char *reg = 0; // specified region
44 void *bed = 0; // BED data structure
45 bam_header_t *h = 0; // BAM header of the 1st input
49 // parse the command line
50 while ((n = getopt(argc, argv, "r:b:q:Q:l:")) >= 0) {
52 case 'l': min_len = atoi(optarg); break; // minimum query length
53 case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header
54 case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
55 case 'q': baseQ = atoi(optarg); break; // base quality threshold
56 case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold
60 fprintf(stderr, "Usage: bam2depth [-r reg] [-q baseQthres] [-Q mapQthres] [-l minQLen] [-b in.bed] <in1.bam> [...]\n");
64 // initialize the auxiliary data structures
65 n = argc - optind; // the number of BAMs on the command line
66 data = calloc(n, sizeof(void*)); // data[i] for the i-th input
67 beg = 0; end = 1<<30; tid = -1; // set the default region
68 for (i = 0; i < n; ++i) {
70 data[i] = calloc(1, sizeof(aux_t));
71 data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM
72 data[i]->min_mapQ = mapQ; // set the mapQ filter
73 data[i]->min_len = min_len; // set the qlen filter
74 htmp = bam_header_read(data[i]->fp); // read the BAM header
76 h = htmp; // keep the header of the 1st BAM
77 if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region
78 } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header
79 if (tid >= 0) { // if a region is specified and parsed successfully
80 bam_index_t *idx = bam_index_load(argv[optind+i]); // load the index
81 data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator
82 bam_index_destroy(idx); // the index is not needed any more; phase out of the memory
86 // the core multi-pileup loop
87 mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
88 n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
89 plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp)
90 while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
91 if (pos < beg || pos >= end) continue; // out of range; skip
92 if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip
93 fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster
94 for (i = 0; i < n; ++i) { // base level filters have to go here
96 for (j = 0; j < n_plp[i]; ++j) {
97 const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know
98 if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos
99 else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality
101 printf("\t%d", n_plp[i] - m); // this the depth to output
105 free(n_plp); free(plp);
106 bam_mplp_destroy(mplp);
108 bam_header_destroy(h);
109 for (i = 0; i < n; ++i) {
110 bam_close(data[i]->fp);
111 if (data[i]->iter) bam_iter_destroy(data[i]->iter);
114 free(data); free(reg);
115 if (bed) bed_destroy(bed);