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