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comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtsw2_main.c @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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-1:000000000000 0:acc2ca1a3ba4
1 #include <unistd.h>
2 #include <stdlib.h>
3 #include <string.h>
4 #include <stdio.h>
5 #include <math.h>
6 #include "bwt.h"
7 #include "bwtsw2.h"
8
9 int bwa_bwtsw2(int argc, char *argv[])
10 {
11 bsw2opt_t *opt;
12 bwt_t *target[2];
13 char buf[1024];
14 bntseq_t *bns;
15 int c;
16
17 opt = bsw2_init_opt();
18 srand48(11);
19 while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:y:s:c:N:H:f:")) >= 0) {
20 switch (c) {
21 case 'q': opt->q = atoi(optarg); break;
22 case 'r': opt->r = atoi(optarg); break;
23 case 'a': opt->a = atoi(optarg); break;
24 case 'b': opt->b = atoi(optarg); break;
25 case 'w': opt->bw = atoi(optarg); break;
26 case 'T': opt->t = atoi(optarg); break;
27 case 't': opt->n_threads = atoi(optarg); break;
28 case 'z': opt->z = atoi(optarg); break;
29 case 'y': opt->yita = atof(optarg); break;
30 case 's': opt->is = atoi(optarg); break;
31 case 'm': opt->mask_level = atof(optarg); break;
32 case 'c': opt->coef = atof(optarg); break;
33 case 'N': opt->t_seeds = atoi(optarg); break;
34 case 'H': opt->hard_clip = 1; break;
35 case 'f': freopen(optarg, "w", stdout);
36 }
37 }
38 opt->qr = opt->q + opt->r;
39
40 if (optind + 2 > argc) {
41 fprintf(stderr, "\n");
42 fprintf(stderr, "Usage: bwa bwasw [options] <target.prefix> <query.fa>\n\n");
43 fprintf(stderr, "Options: -a INT score for a match [%d]\n", opt->a);
44 fprintf(stderr, " -b INT mismatch penalty [%d]\n", opt->b);
45 fprintf(stderr, " -q INT gap open penalty [%d]\n", opt->q);
46 fprintf(stderr, " -r INT gap extension penalty [%d]\n", opt->r);
47 // fprintf(stderr, " -y FLOAT error recurrence coef. (4..16) [%.1f]\n", opt->yita);
48 fprintf(stderr, "\n");
49 fprintf(stderr, " -t INT nmber of threads [%d]\n", opt->n_threads);
50 fprintf(stderr, " -s INT size of a chunk of reads [%d]\n", opt->chunk_size);
51 fprintf(stderr, "\n");
52 fprintf(stderr, " -w INT band width [%d]\n", opt->bw);
53 fprintf(stderr, " -m FLOAT mask level [%.2f]\n", opt->mask_level);
54 fprintf(stderr, "\n");
55 fprintf(stderr, " -T INT score threshold divided by a [%d]\n", opt->t);
56 fprintf(stderr, " -s INT maximum seeding interval size [%d]\n", opt->is);
57 fprintf(stderr, " -z INT Z-best [%d]\n", opt->z);
58 fprintf(stderr, " -N INT # seeds to trigger reverse alignment [%d]\n", opt->t_seeds);
59 fprintf(stderr, " -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
60 fprintf(stderr, " -H in SAM output, use hard clipping rather than soft\n");
61 fprintf(stderr, " -f FILE file to output results to instead of stdout\n");
62 fprintf(stderr, "\n");
63
64 {
65 double c, theta, eps, delta;
66 c = opt->a / log(opt->yita);
67 theta = exp(-opt->b / c) / opt->yita;
68 eps = exp(-opt->q / c);
69 delta = exp(-opt->r / c);
70 fprintf(stderr, "mismatch: %lf, gap_open: %lf, gap_ext: %lf\n\n",
71 theta, eps, delta);
72 }
73 return 1;
74 }
75
76 // adjust opt for opt->a
77 opt->t *= opt->a;
78 opt->coef *= opt->a;
79
80 strcpy(buf, argv[optind]); target[0] = bwt_restore_bwt(strcat(buf, ".bwt"));
81 strcpy(buf, argv[optind]); bwt_restore_sa(strcat(buf, ".sa"), target[0]);
82 strcpy(buf, argv[optind]); target[1] = bwt_restore_bwt(strcat(buf, ".rbwt"));
83 strcpy(buf, argv[optind]); bwt_restore_sa(strcat(buf, ".rsa"), target[1]);
84 bns = bns_restore(argv[optind]);
85
86 bsw2_aln(opt, bns, target, argv[optind+1]);
87
88 bns_destroy(bns);
89 bwt_destroy(target[0]); bwt_destroy(target[1]);
90 free(opt);
91
92 return 0;
93 }