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comparison PsiCLASS-1.0.2/samtools-0.1.19/bam2depth.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 /* 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:
4 *
5 * gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -L. -lbam -lz
6 */
7 #include <stdlib.h>
8 #include <string.h>
9 #include <stdio.h>
10 #include <unistd.h>
11 #include "bam.h"
12
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
17 } aux_t;
18
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
22
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
25 {
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;
31 }
32 return ret;
33 }
34
35 int read_file_list(const char *file_list,int *n,char **argv[]);
36
37 #ifdef _MAIN_BAM2DEPTH
38 int main(int argc, char *argv[])
39 #else
40 int main_depth(int argc, char *argv[])
41 #endif
42 {
43 int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0, nfiles;
44 const bam_pileup1_t **plp;
45 char *reg = 0; // specified region
46 void *bed = 0; // BED data structure
47 char *file_list = NULL, **fn = NULL;
48 bam_header_t *h = 0; // BAM header of the 1st input
49 aux_t **data;
50 bam_mplp_t mplp;
51
52 // parse the command line
53 while ((n = getopt(argc, argv, "r:b:q:Q:l:f:")) >= 0) {
54 switch (n) {
55 case 'l': min_len = atoi(optarg); break; // minimum query length
56 case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header
57 case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
58 case 'q': baseQ = atoi(optarg); break; // base quality threshold
59 case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold
60 case 'f': file_list = optarg; break;
61 }
62 }
63 if (optind == argc && !file_list) {
64 fprintf(stderr, "\n");
65 fprintf(stderr, "Usage: samtools depth [options] in1.bam [in2.bam [...]]\n");
66 fprintf(stderr, "Options:\n");
67 fprintf(stderr, " -b <bed> list of positions or regions\n");
68 fprintf(stderr, " -f <list> list of input BAM filenames, one per line [null]\n");
69 fprintf(stderr, " -l <int> minQLen\n");
70 fprintf(stderr, " -q <int> base quality threshold\n");
71 fprintf(stderr, " -Q <int> mapping quality threshold\n");
72 fprintf(stderr, " -r <chr:from-to> region\n");
73 fprintf(stderr, "\n");
74 return 1;
75 }
76
77 // initialize the auxiliary data structures
78 if (file_list)
79 {
80 if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
81 n = nfiles;
82 argv = fn;
83 optind = 0;
84 }
85 else
86 n = argc - optind; // the number of BAMs on the command line
87 data = calloc(n, sizeof(void*)); // data[i] for the i-th input
88 beg = 0; end = 1<<30; tid = -1; // set the default region
89 for (i = 0; i < n; ++i) {
90 bam_header_t *htmp;
91 data[i] = calloc(1, sizeof(aux_t));
92 data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM
93 data[i]->min_mapQ = mapQ; // set the mapQ filter
94 data[i]->min_len = min_len; // set the qlen filter
95 htmp = bam_header_read(data[i]->fp); // read the BAM header
96 if (i == 0) {
97 h = htmp; // keep the header of the 1st BAM
98 if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region
99 } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header
100 if (tid >= 0) { // if a region is specified and parsed successfully
101 bam_index_t *idx = bam_index_load(argv[optind+i]); // load the index
102 data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator
103 bam_index_destroy(idx); // the index is not needed any more; phase out of the memory
104 }
105 }
106
107 // the core multi-pileup loop
108 mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
109 n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
110 plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp)
111 while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
112 if (pos < beg || pos >= end) continue; // out of range; skip
113 if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip
114 fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster
115 for (i = 0; i < n; ++i) { // base level filters have to go here
116 int j, m = 0;
117 for (j = 0; j < n_plp[i]; ++j) {
118 const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know
119 if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos
120 else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality
121 }
122 printf("\t%d", n_plp[i] - m); // this the depth to output
123 }
124 putchar('\n');
125 }
126 free(n_plp); free(plp);
127 bam_mplp_destroy(mplp);
128
129 bam_header_destroy(h);
130 for (i = 0; i < n; ++i) {
131 bam_close(data[i]->fp);
132 if (data[i]->iter) bam_iter_destroy(data[i]->iter);
133 free(data[i]);
134 }
135 free(data); free(reg);
136 if (bed) bed_destroy(bed);
137 if ( file_list )
138 {
139 for (i=0; i<n; i++) free(fn[i]);
140 free(fn);
141 }
142 return 0;
143 }