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1 #include <stdio.h>
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2 #include <unistd.h>
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3 #include <math.h>
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4 #include <stdlib.h>
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5 #include <string.h>
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6 #include <time.h>
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7 #include <stdint.h>
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8 #ifdef HAVE_CONFIG_H
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9 #include "config.h"
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10 #endif
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11 #include "bwtaln.h"
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12 #include "bwtgap.h"
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13 #include "utils.h"
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14
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15 #ifdef HAVE_PTHREAD
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16 #define THREAD_BLOCK_SIZE 1024
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17 #include <pthread.h>
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18 static pthread_mutex_t g_seq_lock = PTHREAD_MUTEX_INITIALIZER;
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19 #endif
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20
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21 gap_opt_t *gap_init_opt()
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22 {
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23 gap_opt_t *o;
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24 o = (gap_opt_t*)calloc(1, sizeof(gap_opt_t));
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25 /* IMPORTANT: s_mm*10 should be about the average base error
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26 rate. Voilating this requirement will break pairing! */
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27 o->s_mm = 3; o->s_gapo = 11; o->s_gape = 4;
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28 o->max_diff = -1; o->max_gapo = 1; o->max_gape = 6;
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29 o->indel_end_skip = 5; o->max_del_occ = 10; o->max_entries = 2000000;
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30 o->mode = BWA_MODE_GAPE | BWA_MODE_COMPREAD;
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31 o->seed_len = 32; o->max_seed_diff = 2;
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32 o->fnr = 0.04;
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33 o->n_threads = 1;
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34 o->max_top2 = 30;
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35 o->trim_qual = 0;
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36 return o;
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37 }
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38
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39 int bwa_cal_maxdiff(int l, double err, double thres)
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40 {
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41 double elambda = exp(-l * err);
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42 double sum, y = 1.0;
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43 int k, x = 1;
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44 for (k = 1, sum = elambda; k < 1000; ++k) {
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45 y *= l * err;
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46 x *= k;
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47 sum += elambda * y / x;
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48 if (1.0 - sum < thres) return k;
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49 }
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50 return 2;
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51 }
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52
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53 // width must be filled as zero
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54 static int bwt_cal_width(const bwt_t *rbwt, int len, const ubyte_t *str, bwt_width_t *width)
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55 {
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56 bwtint_t k, l, ok, ol;
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57 int i, bid;
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58 bid = 0;
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59 k = 0; l = rbwt->seq_len;
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60 for (i = 0; i < len; ++i) {
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61 ubyte_t c = str[i];
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62 if (c < 4) {
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63 bwt_2occ(rbwt, k - 1, l, c, &ok, &ol);
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64 k = rbwt->L2[c] + ok + 1;
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65 l = rbwt->L2[c] + ol;
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66 }
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67 if (k > l || c > 3) { // then restart
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68 k = 0;
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69 l = rbwt->seq_len;
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70 ++bid;
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71 }
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72 width[i].w = l - k + 1;
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73 width[i].bid = bid;
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74 }
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75 width[len].w = 0;
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76 width[len].bid = ++bid;
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77 return bid;
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78 }
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79
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80 void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt[2], int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt)
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81 {
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82 int i, max_l = 0, max_len;
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83 gap_stack_t *stack;
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84 bwt_width_t *w[2], *seed_w[2];
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85 const ubyte_t *seq[2];
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86 gap_opt_t local_opt = *opt;
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87
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88 // initiate priority stack
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89 for (i = max_len = 0; i != n_seqs; ++i)
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90 if (seqs[i].len > max_len) max_len = seqs[i].len;
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91 if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(max_len, BWA_AVG_ERR, opt->fnr);
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92 if (local_opt.max_diff < local_opt.max_gapo) local_opt.max_gapo = local_opt.max_diff;
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93 stack = gap_init_stack(local_opt.max_diff, local_opt.max_gapo, local_opt.max_gape, &local_opt);
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94
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95 seed_w[0] = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
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96 seed_w[1] = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
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97 w[0] = w[1] = 0;
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98 for (i = 0; i != n_seqs; ++i) {
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99 bwa_seq_t *p = seqs + i;
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100 #ifdef HAVE_PTHREAD
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101 if (opt->n_threads > 1) {
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102 pthread_mutex_lock(&g_seq_lock);
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103 if (p->tid < 0) { // unassigned
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104 int j;
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105 for (j = i; j < n_seqs && j < i + THREAD_BLOCK_SIZE; ++j)
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106 seqs[j].tid = tid;
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107 } else if (p->tid != tid) {
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108 pthread_mutex_unlock(&g_seq_lock);
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109 continue;
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110 }
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111 pthread_mutex_unlock(&g_seq_lock);
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112 }
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113 #endif
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114 p->sa = 0; p->type = BWA_TYPE_NO_MATCH; p->c1 = p->c2 = 0; p->n_aln = 0; p->aln = 0;
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115 seq[0] = p->seq; seq[1] = p->rseq;
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116 if (max_l < p->len) {
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117 max_l = p->len;
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118 w[0] = (bwt_width_t*)calloc(max_l + 1, sizeof(bwt_width_t));
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119 w[1] = (bwt_width_t*)calloc(max_l + 1, sizeof(bwt_width_t));
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120 }
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121 bwt_cal_width(bwt[0], p->len, seq[0], w[0]);
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122 bwt_cal_width(bwt[1], p->len, seq[1], w[1]);
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123 if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(p->len, BWA_AVG_ERR, opt->fnr);
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124 local_opt.seed_len = opt->seed_len < p->len? opt->seed_len : 0x7fffffff;
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125 if (p->len > opt->seed_len) {
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126 bwt_cal_width(bwt[0], opt->seed_len, seq[0] + (p->len - opt->seed_len), seed_w[0]);
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127 bwt_cal_width(bwt[1], opt->seed_len, seq[1] + (p->len - opt->seed_len), seed_w[1]);
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128 }
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129 // core function
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130 p->aln = bwt_match_gap(bwt, p->len, seq, w, p->len <= opt->seed_len? 0 : seed_w, &local_opt, &p->n_aln, stack);
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131 // store the alignment
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132 free(p->name); free(p->seq); free(p->rseq); free(p->qual);
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133 p->name = 0; p->seq = p->rseq = p->qual = 0;
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134 }
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135 free(seed_w[0]); free(seed_w[1]);
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136 free(w[0]); free(w[1]);
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137 gap_destroy_stack(stack);
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138 }
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139
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140 #ifdef HAVE_PTHREAD
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141 typedef struct {
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142 int tid;
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143 bwt_t *bwt[2];
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144 int n_seqs;
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145 bwa_seq_t *seqs;
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146 const gap_opt_t *opt;
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147 } thread_aux_t;
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148
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149 static void *worker(void *data)
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150 {
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151 thread_aux_t *d = (thread_aux_t*)data;
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152 bwa_cal_sa_reg_gap(d->tid, d->bwt, d->n_seqs, d->seqs, d->opt);
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153 return 0;
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154 }
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155 #endif
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156
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157 void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
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158 {
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159 int i, n_seqs, tot_seqs = 0;
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160 bwa_seq_t *seqs;
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161 bwa_seqio_t *ks;
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162 clock_t t;
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163 bwt_t *bwt[2];
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164
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165 // initialization
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166 ks = bwa_seq_open(fn_fa);
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167
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168 { // load BWT
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169 char *str = (char*)calloc(strlen(prefix) + 10, 1);
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170 strcpy(str, prefix); strcat(str, ".bwt"); bwt[0] = bwt_restore_bwt(str);
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171 strcpy(str, prefix); strcat(str, ".rbwt"); bwt[1] = bwt_restore_bwt(str);
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172 free(str);
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173 }
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174
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175 // core loop
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176 fwrite(opt, sizeof(gap_opt_t), 1, stdout);
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177 while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode & BWA_MODE_COMPREAD, opt->trim_qual)) != 0) {
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178 tot_seqs += n_seqs;
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179 t = clock();
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180
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181 fprintf(stderr, "[bwa_aln_core] calculate SA coordinate... ");
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182
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183 #ifdef HAVE_PTHREAD
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184 if (opt->n_threads <= 1) { // no multi-threading at all
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185 bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
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186 } else {
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187 pthread_t *tid;
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188 pthread_attr_t attr;
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189 thread_aux_t *data;
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190 int j;
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191 pthread_attr_init(&attr);
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192 pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
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193 data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
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194 tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
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195 for (j = 0; j < opt->n_threads; ++j) {
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196 data[j].tid = j; data[j].bwt[0] = bwt[0]; data[j].bwt[1] = bwt[1];
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197 data[j].n_seqs = n_seqs; data[j].seqs = seqs; data[j].opt = opt;
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198 pthread_create(&tid[j], &attr, worker, data + j);
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199 }
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200 for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
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201 free(data); free(tid);
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202 }
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203 #else
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204 bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
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205 #endif
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206
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207 fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
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208
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209 t = clock();
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210 fprintf(stderr, "[bwa_aln_core] write to the disk... ");
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211 for (i = 0; i < n_seqs; ++i) {
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212 bwa_seq_t *p = seqs + i;
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213 fwrite(&p->n_aln, 4, 1, stdout);
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214 if (p->n_aln) fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
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215 }
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216 fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
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217
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218 bwa_free_read_seq(n_seqs, seqs);
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219 fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
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220 }
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221
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222 // destroy
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223 bwt_destroy(bwt[0]); bwt_destroy(bwt[1]);
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224 bwa_seq_close(ks);
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225 }
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226
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227 int bwa_aln(int argc, char *argv[])
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228 {
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229 int c, opte = -1;
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230 gap_opt_t *opt;
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231
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232 opt = gap_init_opt();
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233 while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:")) >= 0) {
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234 switch (c) {
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235 case 'n':
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236 if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
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237 else opt->max_diff = atoi(optarg), opt->fnr = -1.0;
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238 break;
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239 case 'o': opt->max_gapo = atoi(optarg); break;
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240 case 'e': opte = atoi(optarg); break;
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241 case 'M': opt->s_mm = atoi(optarg); break;
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242 case 'O': opt->s_gapo = atoi(optarg); break;
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243 case 'E': opt->s_gape = atoi(optarg); break;
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244 case 'd': opt->max_del_occ = atoi(optarg); break;
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245 case 'i': opt->indel_end_skip = atoi(optarg); break;
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246 case 'l': opt->seed_len = atoi(optarg); break;
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247 case 'k': opt->max_seed_diff = atoi(optarg); break;
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248 case 'm': opt->max_entries = atoi(optarg); break;
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249 case 't': opt->n_threads = atoi(optarg); break;
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250 case 'L': opt->mode |= BWA_MODE_LOGGAP; break;
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251 case 'R': opt->max_top2 = atoi(optarg); break;
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252 case 'q': opt->trim_qual = atoi(optarg); break;
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253 case 'c': opt->mode &= ~BWA_MODE_COMPREAD; break;
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254 case 'N': opt->mode |= BWA_MODE_NONSTOP; opt->max_top2 = 0x7fffffff; break;
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255 case 'f': freopen(optarg, "wb", stdout); break;
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256 default: return 1;
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257 }
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258 }
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259 if (opte > 0) {
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260 opt->max_gape = opte;
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261 opt->mode &= ~BWA_MODE_GAPE;
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262 }
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263
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264 if (optind + 2 > argc) {
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265 fprintf(stderr, "\n");
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266 fprintf(stderr, "Usage: bwa aln [options] <prefix> <in.fq>\n\n");
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267 fprintf(stderr, "Options: -n NUM max #diff (int) or missing prob under %.2f err rate (float) [%.2f]\n",
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268 BWA_AVG_ERR, opt->fnr);
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269 fprintf(stderr, " -o INT maximum number or fraction of gap opens [%d]\n", opt->max_gapo);
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270 fprintf(stderr, " -e INT maximum number of gap extensions, -1 for disabling long gaps [-1]\n");
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271 fprintf(stderr, " -i INT do not put an indel within INT bp towards the ends [%d]\n", opt->indel_end_skip);
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272 fprintf(stderr, " -d INT maximum occurrences for extending a long deletion [%d]\n", opt->max_del_occ);
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273 fprintf(stderr, " -l INT seed length [%d]\n", opt->seed_len);
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274 fprintf(stderr, " -k INT maximum differences in the seed [%d]\n", opt->max_seed_diff);
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275 fprintf(stderr, " -m INT maximum entries in the queue [%d]\n", opt->max_entries);
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276 fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
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277 fprintf(stderr, " -M INT mismatch penalty [%d]\n", opt->s_mm);
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278 fprintf(stderr, " -O INT gap open penalty [%d]\n", opt->s_gapo);
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279 fprintf(stderr, " -E INT gap extension penalty [%d]\n", opt->s_gape);
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280 fprintf(stderr, " -R INT stop searching when there are >INT equally best hits [%d]\n", opt->max_top2);
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281 fprintf(stderr, " -q INT quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual);
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282 fprintf(stderr, " -c input sequences are in the color space\n");
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283 fprintf(stderr, " -L log-scaled gap penalty for long deletions\n");
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284 fprintf(stderr, " -N non-iterative mode: search for all n-difference hits (slooow)\n");
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285 fprintf(stderr, " -f FILE file to write output to instead of stdout\n");
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286 fprintf(stderr, "\n");
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287 return 1;
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288 }
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289 if (opt->fnr > 0.0) {
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290 int i, k;
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291 for (i = 17, k = 0; i <= 250; ++i) {
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292 int l = bwa_cal_maxdiff(i, BWA_AVG_ERR, opt->fnr);
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293 if (l != k) fprintf(stderr, "[bwa_aln] %dbp reads: max_diff = %d\n", i, l);
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294 k = l;
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295 }
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296 }
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297 bwa_aln_core(argv[optind], argv[optind+1], opt);
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298 free(opt);
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299 return 0;
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300 }
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301
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302 /* rgoya: Temporary clone of aln_path2cigar to accomodate for bwa_cigar_t,
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303 __cigar_op and __cigar_len while keeping stdaln stand alone */
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304 bwa_cigar_t *bwa_aln_path2cigar(const path_t *path, int path_len, int *n_cigar)
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305 {
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306 uint32_t *cigar32;
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307 bwa_cigar_t *cigar;
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308 int i;
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309 cigar32 = aln_path2cigar32((path_t*) path, path_len, n_cigar);
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310 cigar = (bwa_cigar_t*)cigar32;
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311 for (i = 0; i < *n_cigar; ++i)
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312 cigar[i] = __cigar_create( (cigar32[i]&0xf), (cigar32[i]>>4) );
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313 return cigar;
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314 }
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315
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