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1 #include <stdlib.h>
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2 #include <stdio.h>
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3 #include <math.h>
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4 #ifdef HAVE_CONFIG_H
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5 #include "config.h"
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6 #endif
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7 #ifdef HAVE_PTHREAD
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8 #include <pthread.h>
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9 #endif
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10 #include "bntseq.h"
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11 #include "bwt_lite.h"
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12 #include "utils.h"
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13 #include "bwtsw2.h"
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14 #include "stdaln.h"
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15 #include "kstring.h"
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16
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17 #include "kseq.h"
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18 KSEQ_INIT(gzFile, gzread)
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19
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20 #include "ksort.h"
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21 #define __left_lt(a, b) ((a).end > (b).end)
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22 KSORT_INIT(hit, bsw2hit_t, __left_lt)
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23
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24 extern unsigned char nst_nt4_table[256];
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25
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26 unsigned char nt_comp_table[256] = {
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27 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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28 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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29 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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30 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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31 'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N',
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32 'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N',
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33 'n','t','v','g', 'h','n','n','c', 'd','n','n','m', 'n','k','n','n',
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34 'n','n','y','s', 'a','n','b','w', 'x','r','n','N', 'N','N','N','N',
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35 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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36 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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37 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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38 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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39 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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40 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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41 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
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42 'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N'
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43 };
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44
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45 extern int bsw2_resolve_duphits(const bwt_t *bwt, bwtsw2_t *b, int IS);
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46 extern int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level);
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47
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48 bsw2opt_t *bsw2_init_opt()
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49 {
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50 bsw2opt_t *o = (bsw2opt_t*)calloc(1, sizeof(bsw2opt_t));
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51 o->a = 1; o->b = 3; o->q = 5; o->r = 2; o->t = 30;
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52 o->bw = 50;
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53 o->z = 1; o->is = 3; o->t_seeds = 5; o->hard_clip = 0;
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54 o->mask_level = 0.50f; o->yita = 5.5f; o->coef = 5.5f;
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55 o->qr = o->q + o->r; o->n_threads = 1; o->chunk_size = 10000000;
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56 return o;
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57 }
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58
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59 void bsw2_destroy(bwtsw2_t *b)
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60 {
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61 int i;
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62 if (b == 0) return;
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63 if (b->cigar)
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64 for (i = 0; i < b->n; ++i) free(b->cigar[i]);
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65 free(b->cigar); free(b->n_cigar); free(b->hits);
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66 free(b);
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67 }
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68
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69 #define __gen_ap(par, opt) do { \
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70 int i; \
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71 for (i = 0; i < 25; ++i) (par).matrix[i] = -(opt)->b; \
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72 for (i = 0; i < 4; ++i) (par).matrix[i*5+i] = (opt)->a; \
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73 (par).gap_open = (opt)->q; (par).gap_ext = (opt)->r; \
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74 (par).gap_end = (opt)->r; \
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75 (par).row = 5; (par).band_width = opt->bw; \
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76 } while (0)
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77
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78 #define __rpac(pac, l, i) (pac[(l-i-1)>>2] >> (~(l-i-1)&3)*2 & 0x3)
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79
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80 void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq, uint8_t *pac, uint32_t l_pac, int is_rev, uint8_t *_mem)
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81 {
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82 int i, matrix[25];
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83 bwtint_t k;
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84 uint8_t *target = 0, *query;
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85 AlnParam par;
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86
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87 par.matrix = matrix;
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88 __gen_ap(par, opt);
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89 query = calloc(lq, 1);
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90 // sort according to the descending order of query end
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91 ks_introsort(hit, b->n, b->hits);
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92 target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
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93 // reverse _query
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94 for (i = 0; i < lq; ++i) query[lq - i - 1] = _query[i];
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95 // core loop
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96 for (i = 0; i < b->n; ++i) {
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97 bsw2hit_t *p = b->hits + i;
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98 int lt = ((p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
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99 int score, j;
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100 path_t path;
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101 p->n_seeds = 1;
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102 if (p->l || p->k == 0) continue;
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103 for (j = score = 0; j < i; ++j) {
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104 bsw2hit_t *q = b->hits + j;
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105 if (q->beg <= p->beg && q->k <= p->k && q->k + q->len >= p->k + p->len) {
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106 if (q->n_seeds < (1<<14) - 2) ++q->n_seeds;
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107 ++score;
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108 }
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109 }
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110 if (score) continue;
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111 if (lt > p->k) lt = p->k;
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112 if (is_rev) {
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113 for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
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114 target[j++] = __rpac(pac, l_pac, k);
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115 } else {
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116 for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
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117 target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
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118 }
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119 lt = j;
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120 score = aln_extend_core(target, lt, query + lq - p->beg, p->beg, &par, &path, 0, p->G, _mem);
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121 if (score > p->G) { // extensible
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122 p->G = score;
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123 p->len += path.i;
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124 p->beg -= path.j;
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125 p->k -= path.i;
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126 }
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127 }
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128 free(query); free(target);
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129 }
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130
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131 void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq, uint8_t *pac, uint32_t l_pac, int is_rev, uint8_t *_mem)
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132 {
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133 int i, matrix[25];
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134 uint32_t k;
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135 uint8_t *target;
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136 AlnParam par;
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137
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138 par.matrix = matrix;
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139 __gen_ap(par, opt);
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140 target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
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141 for (i = 0; i < b->n; ++i) {
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142 bsw2hit_t *p = b->hits + i;
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143 int lt = ((lq - p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
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144 int j, score;
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145 path_t path;
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146 if (p->l) continue;
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147 if (is_rev) {
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148 for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
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149 target[j++] = __rpac(pac, l_pac, k);
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150 } else {
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151 for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
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152 target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
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153 }
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154 lt = j;
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155 score = aln_extend_core(target, lt, query + p->beg, lq - p->beg, &par, &path, 0, 1, _mem);
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156 // if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
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157 if (score >= p->G) {
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158 p->G = score;
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159 p->len = path.i;
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160 p->end = path.j + p->beg;
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161 }
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162 }
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163 free(target);
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164 }
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165
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166 /* generate CIGAR array(s) in b->cigar[] */
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167 static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], uint8_t *pac, bwtsw2_t *b)
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168 {
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169 uint8_t *target;
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170 int i, matrix[25];
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171 AlnParam par;
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172 path_t *path;
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173
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174 par.matrix = matrix;
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175 __gen_ap(par, opt);
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176 i = ((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq; // maximum possible target length
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177 target = calloc(i, 1);
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178 path = calloc(i + lq, sizeof(path_t));
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179 // memory clean up for b
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180 if (b->n < b->max) {
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181 b->max = b->n;
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182 b->hits = realloc(b->hits, b->n * sizeof(bsw2hit_t));
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183 }
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184 if (b->cigar) free(b->cigar);
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185 if (b->n_cigar) free(b->n_cigar);
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186 b->cigar = (uint32_t**)calloc(b->max, sizeof(void*));
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187 b->n_cigar = (int*)calloc(b->max, sizeof(int));
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188 // generate CIGAR
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189 for (i = 0; i < b->n; ++i) {
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190 bsw2hit_t *p = b->hits + i;
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191 uint8_t *query;
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192 uint32_t k;
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193 int score, path_len, beg, end;
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194 if (p->l) continue;
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195 beg = (p->flag & 0x10)? lq - p->end : p->beg;
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196 end = (p->flag & 0x10)? lq - p->beg : p->end;
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197 query = seq[(p->flag & 0x10)? 1 : 0] + beg;
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198 for (k = p->k; k < p->k + p->len; ++k) // in principle, no out-of-boundary here
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199 target[k - p->k] = pac[k>>2] >> (~k&3)*2 & 0x3;
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200 score = aln_global_core(target, p->len, query, end - beg, &par, path, &path_len);
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201 b->cigar[i] = aln_path2cigar32(path, path_len, &b->n_cigar[i]);
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202 if (beg != 0 || end < lq) { // write soft clipping
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203 b->cigar[i] = realloc(b->cigar[i], 4 * (b->n_cigar[i] + 2));
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204 if (beg != 0) {
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205 memmove(b->cigar[i] + 1, b->cigar[i], b->n_cigar[i] * 4);
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206 b->cigar[i][0] = beg<<4 | 4;
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207 ++b->n_cigar[i];
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208 }
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209 if (end < lq) {
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210 b->cigar[i][b->n_cigar[i]] = (lq - end)<<4 | 4;
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211 ++b->n_cigar[i];
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212 }
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213 }
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214 }
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215 free(target); free(path);
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216 }
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217
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218 /* this is for the debugging purpose only */
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219 void bsw2_debug_hits(const bwtsw2_t *b)
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220 {
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221 int i;
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222 printf("# raw hits: %d\n", b->n);
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223 for (i = 0; i < b->n; ++i) {
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224 bsw2hit_t *p = b->hits + i;
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225 if (p->l == 0)
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226 printf("%d, %d, %d, %u, %u\n", p->G, p->beg, p->end, p->k, p->l);
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227 }
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228 }
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229
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230 static void merge_hits(bwtsw2_t *b[2], int l, int is_reverse)
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231 {
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232 int i;
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233 if (b[0]->n + b[1]->n > b[0]->max) {
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234 b[0]->max = b[0]->n + b[1]->n;
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235 b[0]->hits = realloc(b[0]->hits, b[0]->max * sizeof(bsw2hit_t));
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236 }
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237 for (i = 0; i < b[1]->n; ++i) {
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238 bsw2hit_t *p = b[0]->hits + b[0]->n + i;
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239 *p = b[1]->hits[i];
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240 if (is_reverse) {
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241 int x = p->beg;
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242 p->beg = l - p->end;
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243 p->end = l - x;
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244 p->flag |= 0x10;
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245 }
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246 }
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247 b[0]->n += b[1]->n;
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248 bsw2_destroy(b[1]);
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249 b[1] = 0;
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250 }
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251
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252 static bwtsw2_t *bsw2_aln1_core(const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target, int l, uint8_t *seq[2], int is_rev, bsw2global_t *pool)
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253 {
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254 extern void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2]);
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255 bwtsw2_t *b[2], **bb[2];
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256 int k;
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257 for (k = 0; k < 2; ++k) {
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258 bwtl_t *query = bwtl_seq2bwtl(l, seq[k]);
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259 bb[k] = bsw2_core(opt, query, target, pool);
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260 bwtl_destroy(query);
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261 }
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262 b[0] = bb[0][1]; b[1] = bb[1][1];
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263 bsw2_chain_filter(opt, l, b);
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264 for (k = 0; k < 2; ++k) {
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265 bsw2_extend_left(opt, bb[k][1], seq[k], l, pac, bns->l_pac, is_rev, pool->aln_mem);
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266 merge_hits(bb[k], l, 0);
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267 bsw2_resolve_duphits(0, bb[k][0], 0);
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268 bsw2_extend_rght(opt, bb[k][0], seq[k], l, pac, bns->l_pac, is_rev, pool->aln_mem);
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269 b[k] = bb[k][0];
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270 free(bb[k]);
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271 }
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272 merge_hits(b, l, 1);
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273 bsw2_resolve_query_overlaps(b[0], opt->mask_level);
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274 return b[0];
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275 }
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276
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277 /* set ->flag to records the origin of the hit (to forward bwt or reverse bwt) */
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278 static void flag_fr(bwtsw2_t *b[2])
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279 {
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280 int i, j;
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281 for (i = 0; i < b[0]->n; ++i) {
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282 bsw2hit_t *p = b[0]->hits + i;
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283 p->flag |= 0x10000;
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284 }
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285 for (i = 0; i < b[1]->n; ++i) {
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286 bsw2hit_t *p = b[1]->hits + i;
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287 p->flag |= 0x20000;
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288 }
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289 for (i = 0; i < b[0]->n; ++i) {
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290 bsw2hit_t *p = b[0]->hits + i;
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291 for (j = 0; j < b[1]->n; ++j) {
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292 bsw2hit_t *q = b[1]->hits + i;
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293 if (q->beg == p->beg && q->end == p->end && q->k == p->k && q->len == p->len && q->G == p->G) {
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294 q->flag |= 0x30000; p->flag |= 0x30000;
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295 break;
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296 }
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297 }
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298 }
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299 }
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300
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301 typedef struct {
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302 int l, tid;
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303 char *name, *seq, *qual, *sam;
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304 } bsw2seq1_t;
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305
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306 typedef struct {
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307 int n, max;
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308 bsw2seq1_t *seq;
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309 } bsw2seq_t;
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310
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311 #ifdef HAVE_PTHREAD
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312 static pthread_mutex_t g_dbwtsw_lock = PTHREAD_MUTEX_INITIALIZER;
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313 #endif
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314
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315 static int fix_cigar(const char *qname, const bntseq_t *bns, bsw2hit_t *p, int n_cigar, uint32_t *cigar)
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316 {
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317 // FIXME: this routine does not work if the query bridge three reference sequences
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318 int32_t coor, refl, lq;
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319 int x, y, i, seqid;
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320 bns_coor_pac2real(bns, p->k, p->len, &seqid);
|
|
|
321 coor = p->k - bns->anns[seqid].offset;
|
|
|
322 refl = bns->anns[seqid].len;
|
|
|
323 x = coor; y = 0;
|
|
|
324 // test if the alignment goes beyond the boundary
|
|
|
325 for (i = 0; i < n_cigar; ++i) {
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|
|
326 int op = cigar[i]&0xf, ln = cigar[i]>>4;
|
|
|
327 if (op == 1 || op == 4 || op == 5) y += ln;
|
|
|
328 else if (op == 2) x += ln;
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|
|
329 else x += ln, y += ln;
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|
|
330 }
|
|
|
331 lq = y; // length of the query sequence
|
|
|
332 if (x > refl) { // then fix it
|
|
|
333 int j, nc, mq[2], nlen[2];
|
|
|
334 uint32_t *cn, kk = 0;
|
|
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335 nc = mq[0] = mq[1] = nlen[0] = nlen[1] = 0;
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|
|
336 cn = calloc(n_cigar + 3, 4);
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|
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337 x = coor; y = 0;
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|
|
338 for (i = j = 0; i < n_cigar; ++i) {
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339 int op = cigar[i]&0xf, ln = cigar[i]>>4;
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|
340 if (op == 4 || op == 5 || op == 1) { // ins or clipping
|
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341 y += ln;
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|
|
342 cn[j++] = cigar[i];
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|
|
343 } else if (op == 2) { // del
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|
|
344 if (x + ln >= refl && nc == 0) {
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|
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345 cn[j++] = (uint32_t)(lq - y)<<4 | 4;
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|
346 nc = j;
|
|
|
347 cn[j++] = (uint32_t)y<<4 | 4;
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|
|
348 kk = p->k + (x + ln - refl);
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|
|
349 nlen[0] = x - coor;
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|
|
350 nlen[1] = p->len - nlen[0] - ln;
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|
351 } else cn[j++] = cigar[i];
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|
|
352 x += ln;
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|
|
353 } else if (op == 0) { // match
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|
354 if (x + ln >= refl && nc == 0) {
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355 // FIXME: not consider a special case where a split right between M and I
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|
|
356 cn[j++] = (uint32_t)(refl - x)<<4 | 0; // write M
|
|
|
357 cn[j++] = (uint32_t)(lq - y - (refl - x))<<4 | 4; // write S
|
|
|
358 nc = j;
|
|
|
359 mq[0] += refl - x;
|
|
|
360 cn[j++] = (uint32_t)(y + (refl - x))<<4 | 4;
|
|
|
361 if (x + ln - refl) cn[j++] = (uint32_t)(x + ln - refl)<<4 | 0;
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|
|
362 mq[1] += x + ln - refl;
|
|
|
363 kk = bns->anns[seqid].offset + refl;
|
|
|
364 nlen[0] = refl - coor;
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|
|
365 nlen[1] = p->len - nlen[0];
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|
|
366 } else {
|
|
|
367 cn[j++] = cigar[i];
|
|
|
368 mq[nc?1:0] += ln;
|
|
|
369 }
|
|
|
370 x += ln; y += ln;
|
|
|
371 }
|
|
|
372 }
|
|
|
373 if (mq[0] > mq[1]) { // then take the first alignment
|
|
|
374 n_cigar = nc;
|
|
|
375 memcpy(cigar, cn, 4 * nc);
|
|
|
376 p->len = nlen[0];
|
|
|
377 } else {
|
|
|
378 p->k = kk; p->len = nlen[1];
|
|
|
379 n_cigar = j - nc;
|
|
|
380 memcpy(cigar, cn + nc, 4 * (j - nc));
|
|
|
381 }
|
|
|
382 free(cn);
|
|
|
383 }
|
|
|
384 return n_cigar;
|
|
|
385 }
|
|
|
386
|
|
|
387 /* generate SAM lines for a sequence in ks with alignment stored in
|
|
|
388 * b. ks->name and ks->seq will be freed and set to NULL in the end. */
|
|
|
389 static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks, bwtsw2_t *b)
|
|
|
390 {
|
|
|
391 int i, k;
|
|
|
392 kstring_t str;
|
|
|
393 memset(&str, 0, sizeof(kstring_t));
|
|
|
394 for (i = 0; i < b->n; ++i) {
|
|
|
395 bsw2hit_t *p = b->hits + i;
|
|
|
396 int32_t seqid = -1, coor = -1;
|
|
|
397 int j, qual, nn = 0;
|
|
|
398 int beg, end;
|
|
|
399 if (p->l == 0) {
|
|
|
400 b->n_cigar[i] = fix_cigar(ks->name, bns, p, b->n_cigar[i], b->cigar[i]);
|
|
|
401 nn = bns_coor_pac2real(bns, p->k, p->len, &seqid);
|
|
|
402 coor = p->k - bns->anns[seqid].offset;
|
|
|
403 }
|
|
|
404 ksprintf(&str, "%s\t%d", ks->name, p->flag&0x10);
|
|
|
405 ksprintf(&str, "\t%s\t%d", seqid>=0? bns->anns[seqid].name : "*", coor + 1);
|
|
|
406 if (p->l == 0) {
|
|
|
407 { // estimate mapping quality
|
|
|
408 float c = 1.0;
|
|
|
409 int subo = p->G2 > opt->t? p->G2 : opt->t;
|
|
|
410 if (p->flag>>16 == 1 || p->flag>>16 == 2) c *= .5;
|
|
|
411 if (p->n_seeds < 2) c *= .2;
|
|
|
412 qual = (int)(c * (p->G - subo) * (250.0 / p->G + 0.03 / opt->a) + .499);
|
|
|
413 if (qual > 250) qual = 250;
|
|
|
414 if (p->flag&1) qual = 0;
|
|
|
415 }
|
|
|
416 ksprintf(&str, "\t%d\t", qual);
|
|
|
417 for (k = 0; k < b->n_cigar[i]; ++k)
|
|
|
418 ksprintf(&str, "%d%c", b->cigar[i][k]>>4, (opt->hard_clip? "MIDNHHP" : "MIDNSHP")[b->cigar[i][k]&0xf]);
|
|
|
419 } else ksprintf(&str, "\t0\t*");
|
|
|
420 ksprintf(&str, "\t*\t0\t0\t");
|
|
|
421 beg = 0; end = ks->l;
|
|
|
422 if (opt->hard_clip) {
|
|
|
423 if ((b->cigar[i][0]&0xf) == 4) beg += b->cigar[i][0]>>4;
|
|
|
424 if ((b->cigar[i][b->n_cigar[i]-1]&0xf) == 4) end -= b->cigar[i][b->n_cigar[i]-1]>>4;
|
|
|
425 }
|
|
|
426 for (j = beg; j < end; ++j) {
|
|
|
427 if (p->flag&0x10) kputc(nt_comp_table[(int)ks->seq[ks->l - 1 - j]], &str);
|
|
|
428 else kputc(ks->seq[j], &str);
|
|
|
429 }
|
|
|
430 if (ks->qual) {
|
|
|
431 kputc('\t', &str);
|
|
|
432 for (j = beg; j < end; ++j) {
|
|
|
433 if (p->flag&0x10) kputc(ks->qual[ks->l - 1 - j], &str);
|
|
|
434 else kputc(ks->qual[j], &str);
|
|
|
435 }
|
|
|
436 } else ksprintf(&str, "\t*");
|
|
|
437 ksprintf(&str, "\tAS:i:%d\tXS:i:%d\tXF:i:%d\tXE:i:%d\tXN:i:%d", p->G, p->G2, p->flag>>16, p->n_seeds, nn);
|
|
|
438 if (p->l) ksprintf(&str, "\tXI:i:%d", p->l - p->k + 1);
|
|
|
439 kputc('\n', &str);
|
|
|
440 }
|
|
|
441 ks->sam = str.s;
|
|
|
442 free(ks->seq); ks->seq = 0;
|
|
|
443 free(ks->qual); ks->qual = 0;
|
|
|
444 free(ks->name); ks->name = 0;
|
|
|
445 }
|
|
|
446
|
|
|
447 /* Core routine to align reads in _seq. It is separated from
|
|
|
448 * process_seqs() to realize multi-threading */
|
|
|
449 static void bsw2_aln_core(int tid, bsw2seq_t *_seq, const bsw2opt_t *_opt, const bntseq_t *bns, uint8_t *pac, bwt_t * const target[2])
|
|
|
450 {
|
|
|
451 int x;
|
|
|
452 bsw2opt_t opt = *_opt;
|
|
|
453 bsw2global_t *pool = bsw2_global_init();
|
|
|
454 for (x = 0; x < _seq->n; ++x) {
|
|
|
455 bsw2seq1_t *p = _seq->seq + x;
|
|
|
456 uint8_t *seq[2], *rseq[2];
|
|
|
457 int i, l, k;
|
|
|
458 bwtsw2_t *b[2];
|
|
|
459 l = p->l;
|
|
|
460
|
|
|
461 #ifdef HAVE_PTHREAD
|
|
|
462 if (_opt->n_threads > 1) {
|
|
|
463 pthread_mutex_lock(&g_dbwtsw_lock);
|
|
|
464 if (p->tid < 0) p->tid = tid;
|
|
|
465 else if (p->tid != tid) {
|
|
|
466 pthread_mutex_unlock(&g_dbwtsw_lock);
|
|
|
467 continue;
|
|
|
468 } // in pinciple else should not happen
|
|
|
469 pthread_mutex_unlock(&g_dbwtsw_lock);
|
|
|
470 }
|
|
|
471 #endif
|
|
|
472
|
|
|
473 // set opt->t
|
|
|
474 opt.t = _opt->t;
|
|
|
475 if (opt.t < log(l) * opt.coef) opt.t = (int)(log(l) * opt.coef + .499);
|
|
|
476 if (pool->max_l < l) { // then enlarge working space for aln_extend_core()
|
|
|
477 int tmp = ((l + 1) / 2 * opt.a + opt.r) / opt.r + l;
|
|
|
478 pool->max_l = l;
|
|
|
479 pool->aln_mem = realloc(pool->aln_mem, (tmp + 2) * 24);
|
|
|
480 }
|
|
|
481 // set opt->bw
|
|
|
482 opt.bw = _opt->bw;
|
|
|
483 k = (l * opt.a - 2 * opt.q) / (2 * opt.r + opt.a);
|
|
|
484 i = (l * opt.a - opt.a - opt.t) / opt.r;
|
|
|
485 if (k > i) k = i;
|
|
|
486 if (k < 1) k = 1; // I do not know if k==0 causes troubles
|
|
|
487 opt.bw = _opt->bw < k? _opt->bw : k;
|
|
|
488 // set seq[2] and rseq[2]
|
|
|
489 seq[0] = calloc(l * 4, 1);
|
|
|
490 seq[1] = seq[0] + l;
|
|
|
491 rseq[0] = seq[1] + l; rseq[1] = rseq[0] + l;
|
|
|
492 // convert sequences to 2-bit representation
|
|
|
493 for (i = k = 0; i < l; ++i) {
|
|
|
494 int c = nst_nt4_table[(int)p->seq[i]];
|
|
|
495 if (c >= 4) { c = (int)(drand48() * 4); ++k; } // FIXME: ambiguous bases are not properly handled
|
|
|
496 seq[0][i] = c;
|
|
|
497 seq[1][l-1-i] = 3 - c;
|
|
|
498 rseq[0][l-1-i] = c;
|
|
|
499 rseq[1][i] = 3 - c;
|
|
|
500 }
|
|
|
501 if (l - k < opt.t) {
|
|
|
502 free(seq[0]); continue;
|
|
|
503 }
|
|
|
504 // alignment
|
|
|
505 b[0] = bsw2_aln1_core(&opt, bns, pac, target[0], l, seq, 0, pool);
|
|
|
506 for (k = 0; k < b[0]->n; ++k)
|
|
|
507 if (b[0]->hits[k].n_seeds < opt.t_seeds) break;
|
|
|
508 if (k < b[0]->n) {
|
|
|
509 b[1] = bsw2_aln1_core(&opt, bns, pac, target[1], l, rseq, 1, pool);
|
|
|
510 for (i = 0; i < b[1]->n; ++i) {
|
|
|
511 bsw2hit_t *p = b[1]->hits + i;
|
|
|
512 int x = p->beg;
|
|
|
513 p->beg = l - p->end;
|
|
|
514 p->end = l - x;
|
|
|
515 if (p->l == 0) p->k = bns->l_pac - (p->k + p->len);
|
|
|
516 }
|
|
|
517 flag_fr(b);
|
|
|
518 merge_hits(b, l, 0);
|
|
|
519 bsw2_resolve_duphits(0, b[0], 0);
|
|
|
520 bsw2_resolve_query_overlaps(b[0], opt.mask_level);
|
|
|
521 } else b[1] = 0;
|
|
|
522 // generate CIGAR and print SAM
|
|
|
523 gen_cigar(&opt, l, seq, pac, b[0]);
|
|
|
524 print_hits(bns, &opt, p, b[0]);
|
|
|
525 // free
|
|
|
526 free(seq[0]);
|
|
|
527 bsw2_destroy(b[0]);
|
|
|
528 }
|
|
|
529 bsw2_global_destroy(pool);
|
|
|
530 }
|
|
|
531
|
|
|
532 #ifdef HAVE_PTHREAD
|
|
|
533 typedef struct {
|
|
|
534 int tid;
|
|
|
535 bsw2seq_t *_seq;
|
|
|
536 const bsw2opt_t *_opt;
|
|
|
537 const bntseq_t *bns;
|
|
|
538 uint8_t *pac;
|
|
|
539 bwt_t *target[2];
|
|
|
540 } thread_aux_t;
|
|
|
541
|
|
|
542 /* another interface to bsw2_aln_core() to facilitate pthread_create() */
|
|
|
543 static void *worker(void *data)
|
|
|
544 {
|
|
|
545 thread_aux_t *p = (thread_aux_t*)data;
|
|
|
546 bsw2_aln_core(p->tid, p->_seq, p->_opt, p->bns, p->pac, p->target);
|
|
|
547 return 0;
|
|
|
548 }
|
|
|
549 #endif
|
|
|
550
|
|
|
551 /* process sequences stored in _seq, generate SAM lines for these
|
|
|
552 * sequences and reset _seq afterwards. */
|
|
|
553 static void process_seqs(bsw2seq_t *_seq, const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, bwt_t * const target[2])
|
|
|
554 {
|
|
|
555 int i;
|
|
|
556
|
|
|
557 #ifdef HAVE_PTHREAD
|
|
|
558 if (opt->n_threads <= 1) {
|
|
|
559 bsw2_aln_core(0, _seq, opt, bns, pac, target);
|
|
|
560 } else {
|
|
|
561 pthread_t *tid;
|
|
|
562 pthread_attr_t attr;
|
|
|
563 thread_aux_t *data;
|
|
|
564 int j;
|
|
|
565 pthread_attr_init(&attr);
|
|
|
566 pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
|
|
|
567 data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
|
|
|
568 tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
|
|
|
569 for (j = 0; j < opt->n_threads; ++j) {
|
|
|
570 thread_aux_t *p = data + j;
|
|
|
571 p->tid = j; p->_seq = _seq; p->_opt = opt; p->bns = bns;
|
|
|
572 p->pac = pac; p->target[0] = target[0]; p->target[1] = target[1];
|
|
|
573 pthread_create(&tid[j], &attr, worker, p);
|
|
|
574 }
|
|
|
575 for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
|
|
|
576 free(data); free(tid);
|
|
|
577 }
|
|
|
578 #else
|
|
|
579 bsw2_aln_core(0, _seq, opt, bns, pac, target);
|
|
|
580 #endif
|
|
|
581
|
|
|
582 // print and reset
|
|
|
583 for (i = 0; i < _seq->n; ++i) {
|
|
|
584 bsw2seq1_t *p = _seq->seq + i;
|
|
|
585 if (p->sam) printf("%s", p->sam);
|
|
|
586 free(p->name); free(p->seq); free(p->qual); free(p->sam);
|
|
|
587 p->tid = -1; p->l = 0;
|
|
|
588 p->name = p->seq = p->qual = p->sam = 0;
|
|
|
589 }
|
|
|
590 fflush(stdout);
|
|
|
591 _seq->n = 0;
|
|
|
592 }
|
|
|
593
|
|
|
594 void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target[2], const char *fn)
|
|
|
595 {
|
|
|
596 gzFile fp;
|
|
|
597 kseq_t *ks;
|
|
|
598 int l, size = 0;
|
|
|
599 uint8_t *pac;
|
|
|
600 bsw2seq_t *_seq;
|
|
|
601
|
|
|
602 pac = calloc(bns->l_pac/4+1, 1);
|
|
|
603 if (pac == 0) {
|
|
|
604 fprintf(stderr, "[bsw2_aln] insufficient memory!\n");
|
|
|
605 return;
|
|
|
606 }
|
|
|
607 for (l = 0; l < bns->n_seqs; ++l)
|
|
|
608 printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[l].name, bns->anns[l].len);
|
|
|
609 fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
|
|
|
610 fp = xzopen(fn, "r");
|
|
|
611 ks = kseq_init(fp);
|
|
|
612 _seq = calloc(1, sizeof(bsw2seq_t));
|
|
|
613 while ((l = kseq_read(ks)) >= 0) {
|
|
|
614 bsw2seq1_t *p;
|
|
|
615 if (_seq->n == _seq->max) {
|
|
|
616 _seq->max = _seq->max? _seq->max<<1 : 1024;
|
|
|
617 _seq->seq = realloc(_seq->seq, _seq->max * sizeof(bsw2seq1_t));
|
|
|
618 }
|
|
|
619 p = &_seq->seq[_seq->n++];
|
|
|
620 p->tid = -1;
|
|
|
621 p->l = l;
|
|
|
622 p->name = strdup(ks->name.s);
|
|
|
623 p->seq = strdup(ks->seq.s);
|
|
|
624 p->qual = ks->qual.l? strdup(ks->qual.s) : 0;
|
|
|
625 p->sam = 0;
|
|
|
626 size += l;
|
|
|
627 if (size > opt->chunk_size) {
|
|
|
628 fprintf(stderr, "[bsw2_aln] read %d sequences (%d bp)...\n", _seq->n, size);
|
|
|
629 process_seqs(_seq, opt, bns, pac, target);
|
|
|
630 size = 0;
|
|
|
631 }
|
|
|
632 }
|
|
|
633 fprintf(stderr, "[bsw2_aln] read %d sequences (%d bp)...\n", _seq->n, size);
|
|
|
634 process_seqs(_seq, opt, bns, pac, target);
|
|
|
635 free(_seq->seq); free(_seq);
|
|
|
636 kseq_destroy(ks);
|
|
|
637 gzclose(fp);
|
|
|
638 free(pac);
|
|
|
639 }
|
