Mercurial > repos > lsong10 > psiclass

comparison PsiCLASS-1.0.2/samtools-0.1.19/examples/chk_indel.c @ 0:903fc43d6227 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:903fc43d6227
1 /* To compile, copy this file to the samtools source code directory and compile with:
2 gcc -g -O2 -Wall chk_indel_rg.c -o chk_indel_rg -Wall -I. -L. -lbam -lz
3 */
4
5 #include <string.h>
6 #include "bam.h"
7
8 typedef struct {
9 long cnt[4]; // short:ins, short:del, long:ins, long:del
10 } rgcnt_t;
11
12 #include "khash.h"
13 KHASH_MAP_INIT_STR(rgcnt, rgcnt_t)
14
15 #define MAX_LEN 127
16 #define Q_THRES 10
17 #define L_THRES 6 // short: <=L_THRES; otherwise long
18
19 int main(int argc, char *argv[])
20 {
21 bamFile fp;
22 bam1_t *b;
23 int i, x;
24 khash_t(rgcnt) *h;
25 khint_t k;
26
27 if (argc == 1) {
28 fprintf(stderr, "Usage: chk_indel_rg <in.bam>\n\n");
29 fprintf(stderr, "Output: filename, RG, #ins-in-short-homopolymer, #del-in-short, #ins-in-long, #del-in-long\n");
30 return 1;
31 }
32
33 h = kh_init(rgcnt);
34 fp = bam_open(argv[1], "r");
35 bam_header_destroy(bam_header_read(fp)); // we do not need the header
36 b = bam_init1();
37
38 while (bam_read1(fp, b) >= 0) {
39 if (b->core.n_cigar >= 3 && b->core.qual >= Q_THRES) {
40 const uint8_t *seq;
41 const uint32_t *cigar = bam1_cigar(b);
42 char *rg;
43 for (i = 0; i < b->core.n_cigar; ++i) // check if there are 1bp indels
44 if (bam_cigar_oplen(cigar[i]) == 1 && (bam_cigar_op(cigar[i]) == BAM_CDEL || bam_cigar_op(cigar[i]) == BAM_CINS))
45 break;
46 if (i == b->core.n_cigar) continue; // no 1bp ins or del
47 if ((rg = (char*)bam_aux_get(b, "RG")) == 0) continue; // no RG tag
48 seq = bam1_seq(b);
49 for (i = x = 0; i < b->core.n_cigar; ++i) {
50 int op = bam_cigar_op(cigar[i]);
51 if (bam_cigar_oplen(cigar[i]) == 1 && (op == BAM_CDEL || op == BAM_CINS)) {
52 int c, j, hrun, which;
53 c = bam1_seqi(seq, x);
54 for (j = x + 1, hrun = 0; j < b->core.l_qseq; ++j, ++hrun) // calculate the hompolymer run length
55 if (bam1_seqi(seq, j) != c) break;
56 k = kh_get(rgcnt, h, rg + 1);
57 if (k == kh_end(h)) { // absent
58 char *key = strdup(rg + 1);
59 k = kh_put(rgcnt, h, key, &c);
60 memset(&kh_val(h, k), 0, sizeof(rgcnt_t));
61 }
62 which = (hrun <= L_THRES? 0 : 1)<<1 | (op == BAM_CINS? 0 : 1);
63 ++kh_val(h, k).cnt[which];
64 }
65 if (bam_cigar_type(op)&1) ++x;
66 }
67 }
68 }
69
70 for (k = 0; k != kh_end(h); ++k) {
71 if (!kh_exist(h, k)) continue;
72 printf("%s\t%s", argv[1], kh_key(h, k));
73 for (i = 0; i < 4; ++i)
74 printf("\t%ld", kh_val(h, k).cnt[i]);
75 putchar('\n');
76 free((char*)kh_key(h, k));
77 }
78
79 bam_destroy1(b);
80 bam_close(fp);
81 kh_destroy(rgcnt, h);
82 return 0;
83 }