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1 /* This program demonstrates how to generate pileup from multiple BAMs
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2 * simutaneously, to achieve random access and to use the BED interface.
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3 * To compile this program separately, you may:
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4 *
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5 * gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -L. -lbam -lz
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6 */
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7 #include <stdlib.h>
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8 #include <string.h>
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9 #include <stdio.h>
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10 #include <unistd.h>
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11 #include "bam.h"
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12
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13 typedef struct { // auxiliary data structure
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14 bamFile fp; // the file handler
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15 bam_iter_t iter; // NULL if a region not specified
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16 int min_mapQ; // mapQ filter
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17 } aux_t;
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18
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19 void *bed_read(const char *fn); // read a BED or position list file
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20 void bed_destroy(void *_h); // destroy the BED data structure
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21 int bed_overlap(const void *_h, const char *chr, int beg, int end); // test if chr:beg-end overlaps
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22
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23 // This function reads a BAM alignment from one BAM file.
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24 static int read_bam(void *data, bam1_t *b) // read level filters better go here to avoid pileup
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25 {
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26 aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
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27 int ret = aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
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28 if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
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29 return ret;
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30 }
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31
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32 #ifdef _MAIN_BAM2DEPTH
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33 int main(int argc, char *argv[])
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34 #else
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35 int main_depth(int argc, char *argv[])
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36 #endif
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37 {
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38 int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0;
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39 const bam_pileup1_t **plp;
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40 char *reg = 0; // specified region
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41 void *bed = 0; // BED data structure
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42 bam_header_t *h = 0; // BAM header of the 1st input
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43 aux_t **data;
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44 bam_mplp_t mplp;
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45
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46 // parse the command line
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47 while ((n = getopt(argc, argv, "r:b:q:Q:")) >= 0) {
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48 switch (n) {
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49 case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header
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50 case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
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51 case 'q': baseQ = atoi(optarg); break; // base quality threshold
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52 case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold
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53 }
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54 }
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55 if (optind == argc) {
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56 fprintf(stderr, "Usage: bam2depth [-r reg] [-q baseQthres] [-Q mapQthres] [-b in.bed] <in1.bam> [...]\n");
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57 return 1;
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58 }
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59
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60 // initialize the auxiliary data structures
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61 n = argc - optind; // the number of BAMs on the command line
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62 data = calloc(n, sizeof(void*)); // data[i] for the i-th input
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63 beg = 0; end = 1<<30; tid = -1; // set the default region
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64 for (i = 0; i < n; ++i) {
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65 bam_header_t *htmp;
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66 data[i] = calloc(1, sizeof(aux_t));
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67 data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM
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68 data[i]->min_mapQ = mapQ; // set the mapQ filter
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69 htmp = bam_header_read(data[i]->fp); // read the BAM header
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70 if (i == 0) {
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71 h = htmp; // keep the header of the 1st BAM
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72 if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region
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73 } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header
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74 if (tid >= 0) { // if a region is specified and parsed successfully
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75 bam_index_t *idx = bam_index_load(argv[optind+i]); // load the index
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76 data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator
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77 bam_index_destroy(idx); // the index is not needed any more; phase out of the memory
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78 }
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79 }
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80
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81 // the core multi-pileup loop
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82 mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
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83 n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
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84 plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp)
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85 while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
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86 if (pos < beg || pos >= end) continue; // out of range; skip
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87 if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip
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88 fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster
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89 for (i = 0; i < n; ++i) { // base level filters have to go here
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90 int j, m = 0;
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91 for (j = 0; j < n_plp[i]; ++j) {
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92 const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know
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93 if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos
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94 else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality
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95 }
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96 printf("\t%d", n_plp[i] - m); // this the depth to output
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97 }
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98 putchar('\n');
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99 }
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100 free(n_plp); free(plp);
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101 bam_mplp_destroy(mplp);
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102
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103 bam_header_destroy(h);
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104 for (i = 0; i < n; ++i) {
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105 bam_close(data[i]->fp);
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106 if (data[i]->iter) bam_iter_destroy(data[i]->iter);
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107 free(data[i]);
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108 }
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109 free(data); free(reg);
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110 if (bed) bed_destroy(bed);
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111 return 0;
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112 }
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