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1 #include <unistd.h>
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2 #include <string.h>
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3 #include <stdio.h>
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4 #include <stdlib.h>
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5 #include <math.h>
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6 #include <time.h>
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7 #include "stdaln.h"
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8 #include "bwase.h"
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9 #include "bwtaln.h"
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10 #include "bntseq.h"
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11 #include "utils.h"
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12 #include "kstring.h"
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13
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14 static int g_log_n[256];
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15
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16 void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
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17 {
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18 int i, cnt, best;
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19 if (n_aln == 0) {
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20 s->type = BWA_TYPE_NO_MATCH;
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21 s->c1 = s->c2 = 0;
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22 return;
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23 }
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24
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25 if (set_main) {
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26 best = aln[0].score;
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27 for (i = cnt = 0; i < n_aln; ++i) {
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28 const bwt_aln1_t *p = aln + i;
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29 if (p->score > best) break;
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30 if (drand48() * (p->l - p->k + 1) > (double)cnt) {
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31 s->n_mm = p->n_mm; s->n_gapo = p->n_gapo; s->n_gape = p->n_gape; s->strand = p->a;
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32 s->score = p->score;
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33 s->sa = p->k + (bwtint_t)((p->l - p->k + 1) * drand48());
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34 }
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35 cnt += p->l - p->k + 1;
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36 }
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37 s->c1 = cnt;
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38 for (; i < n_aln; ++i) cnt += aln[i].l - aln[i].k + 1;
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39 s->c2 = cnt - s->c1;
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40 s->type = s->c1 > 1? BWA_TYPE_REPEAT : BWA_TYPE_UNIQUE;
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41 }
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42
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43 if (n_multi) {
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44 int k, rest, n_occ, z = 0;
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45 for (k = n_occ = 0; k < n_aln; ++k) {
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46 const bwt_aln1_t *q = aln + k;
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47 n_occ += q->l - q->k + 1;
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48 }
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49 if (s->multi) free(s->multi);
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50 if (n_occ > n_multi + 1) { // if there are too many hits, generate none of them
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51 s->multi = 0; s->n_multi = 0;
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52 return;
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53 }
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54 /* The following code is more flexible than what is required
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55 * here. In principle, due to the requirement above, we can
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56 * simply output all hits, but the following samples "rest"
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57 * number of random hits. */
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58 rest = n_occ > n_multi + 1? n_multi + 1 : n_occ; // find one additional for ->sa
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59 s->multi = calloc(rest, rest * sizeof(bwt_multi1_t));
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60 for (k = 0; k < n_aln; ++k) {
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61 const bwt_aln1_t *q = aln + k;
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62 if (q->l - q->k + 1 <= rest) {
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63 bwtint_t l;
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64 for (l = q->k; l <= q->l; ++l) {
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65 s->multi[z].pos = l;
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66 s->multi[z].gap = q->n_gapo + q->n_gape;
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67 s->multi[z].mm = q->n_mm;
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68 s->multi[z++].strand = q->a;
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69 }
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70 rest -= q->l - q->k + 1;
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71 } else { // Random sampling (http://code.activestate.com/recipes/272884/). In fact, we never come here.
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72 int j, i, k;
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73 for (j = rest, i = q->l - q->k + 1, k = 0; j > 0; --j) {
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74 double p = 1.0, x = drand48();
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75 while (x < p) p -= p * j / (i--);
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76 s->multi[z].pos = q->l - i;
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77 s->multi[z].gap = q->n_gapo + q->n_gape;
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78 s->multi[z].mm = q->n_mm;
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79 s->multi[z++].strand = q->a;
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80 }
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81 rest = 0;
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82 break;
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83 }
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84 }
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85 s->n_multi = z;
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86 for (k = z = 0; k < s->n_multi; ++k)
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87 if (s->multi[k].pos != s->sa)
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88 s->multi[z++] = s->multi[k];
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89 s->n_multi = z < n_multi? z : n_multi;
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90 }
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91 }
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92
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93 void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s)
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94 {
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95 bwa_aln2seq_core(n_aln, aln, s, 1, 0);
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96 }
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97
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98 /* *aln points to alignments found for the current sequence, n_aln is the
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99 size of the array pointed to by *aln. Array *s of size n_seq is a collection
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100 of SAM records that must be replicas, i.e. initialized with the same current sequence.
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101 This method updates sequence records in *s with placements recorded in *aln,
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102 until all n_seq replicas are updated. For each separate alignment record in array *aln,
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103 each placement corresponding to this record will be assigned to a separate record in *s
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104 if there are enough elements remaining in *s, otherwise a random subset of the placements will
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105 be assigned to the remaining elements in *s. The total number of best placements and total
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106 number of non-best placements will be computed from the whole array *aln (regardless of whether it
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107 fits completely into *s or not) and assigned to each updated record in *s.
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108 */
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109 void bwa_aln2seq_all(int n_aln, const bwt_aln1_t *aln, int n_seq, bwa_seq_t *s)
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110 {
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111 int i, cnt1, cnt2, j, best, N;
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112 if (n_aln == 0) {
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113 /* there is no match found for *s */
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114 s->type = BWA_TYPE_NO_MATCH;
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115 s->c1 = s->c2 = 0;
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116 return;
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117 }
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118
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119 N = n_seq; // remember the size of the array
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120 best = aln[0].score;
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121
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122 cnt1 = 0; // total number of already processed alignments (i.e. distinct placements, NOT alignment records) with best score
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123 cnt2 = 0; // total number of already processed alignments with inferior score(s)
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124 for (i = 0; i < n_aln && n_seq > 0 ; ++i) {
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125 const bwt_aln1_t *p_aln = aln + i;
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126
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127 int N_aligns = p_aln->l-p_aln->k +1 ; // number of placements (alignments) in the current alignment record p_aln
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128
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129 if (N_aligns <= n_seq) { /* we have space to save all the alignments stored in 'p_aln' */
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130
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131 for ( j = 0 ; j < N_aligns ; j++ ) {
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132
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133 bwa_seq_t * seq = s + cnt1+ cnt2+j ;
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134 seq->n_mm = p_aln->n_mm; seq->n_gapo = p_aln->n_gapo; seq->n_gape = p_aln->n_gape; seq->strand = p_aln->a;
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135 seq->score = p_aln->score;
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136 seq->sa = p_aln->k + j;
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137 }
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138 n_seq -= N_aligns; // we have n_seq slots remaining to store more alignments
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139 } else { // See also: http://code.activestate.com/recipes/272884/
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140 // we have to truncate, so let's select few remaining alignments randomly:
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141 int xj, xi, xk;
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142 for (xj = n_seq, xi = N_aligns, xk = 0; xj > 0; --xj, ++xk) {
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143 double p = 1.0, x = drand48();
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144 while (x < p) p -= p * xj / (xi--);
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145
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146 bwa_seq_t * seq = s+cnt1+cnt2+xk ;
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147 seq->n_mm = p_aln->n_mm; seq->n_gapo = p_aln->n_gapo; seq->n_gape = p_aln->n_gape; seq->strand = p_aln->a;
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148 seq->score = p_aln->score;
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149 seq->sa = p_aln->l - xi;
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150
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151 }
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152 n_seq = 0;
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153 }
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154 // cnt1 + cnt2 is the total count of hits processed so far:
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155 if ( p_aln->score == best ) cnt1 += N_aligns; // we found N_aligns more placements with best score
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156 else cnt2 += N_aligns; // N_aligns more placements with inferior score
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157 }
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158
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159 // we filled all available slots in the array *s, but there can be more alignments
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160 // left; we need to count them:
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161 for (; i < n_aln; ++i) {
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162 if ( aln[i].score == best ) cnt1 += aln[i].l-aln[i].k+1;
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163 else cnt2 += aln[i].l-aln[i].k+1;
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164 }
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165
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166 // now cnt1 is the total number of found alignments (placements) with best score
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167 // and cnt2 is the total number of found placements with worse score
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168
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169 /* set counts and flags for all hits: */
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170 for (i = 0; i < N ; ++i) {
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171 bwa_seq_t * seq = s+i ;
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172
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173 seq->c1 = cnt1;
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174 seq->c2 = cnt2;
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175 seq->type = seq->c1 > 1? BWA_TYPE_REPEAT : BWA_TYPE_UNIQUE;
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176 }
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177 }
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178
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179
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180
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181 int bwa_approx_mapQ(const bwa_seq_t *p, int mm)
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182 {
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183 int n;
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184 if (p->c1 == 0) return 23;
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185 if (p->c1 > 1) return 0;
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186 if (p->n_mm == mm) return 25;
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187 if (p->c2 == 0) return 37;
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188 n = (p->c2 >= 255)? 255 : p->c2;
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189 return (23 < g_log_n[n])? 0 : 23 - g_log_n[n];
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190 }
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191
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192 /**
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193 * Derive the actual position in the read from the given suffix array
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194 * coordinates. Note that the position will be approximate based on
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195 * whether indels appear in the read and whether calculations are
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196 * performed from the start or end of the read.
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197 */
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198 void bwa_cal_pac_pos_core(const bwt_t *forward_bwt, const bwt_t *reverse_bwt, int n_seqs, bwa_seq_t *s, const int max_mm, const float fnr)
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199 {
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200 int max_diff;
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201 bwa_seq_t *seq;
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202 int i;
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203
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204 for ( i = 0 ; i < n_seqs ; i++ ) {
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205 seq = s + i;
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206 if (seq->type != BWA_TYPE_UNIQUE && seq->type != BWA_TYPE_REPEAT) continue;
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207
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208 max_diff = fnr > 0.0? bwa_cal_maxdiff(seq->len, BWA_AVG_ERR, fnr) : max_mm;
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209 if (seq->strand) { // reverse strand only
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210 seq->pos = bwt_sa(forward_bwt, seq->sa);
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211 seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
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212 } else { // forward strand only
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213 /* NB: For gapped alignment, p->pos may not be correct, which
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214 * will be fixed in refine_gapped_core(). This line also
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215 * determines the way "x" is calculated in
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216 * refine_gapped_core() when (ext < 0 && is_end == 0). */
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217 seq->pos = reverse_bwt->seq_len - (bwt_sa(reverse_bwt, seq->sa) + seq->len);
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218 seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
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219 }
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220 }
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221 }
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222
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223 void bwa_cal_pac_pos(const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr)
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224 {
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225 int i, j;
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226 char str[1024];
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227 bwt_t *bwt;
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228 // load forward SA
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229 strcpy(str, prefix); strcat(str, ".bwt"); bwt = bwt_restore_bwt(str);
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230 strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
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231 for (i = 0; i != n_seqs; ++i) {
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232 if (seqs[i].strand) bwa_cal_pac_pos_core(bwt, 0, 1, &seqs[i], max_mm, fnr);
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233 for (j = 0; j < seqs[i].n_multi; ++j) {
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234 bwt_multi1_t *p = seqs[i].multi + j;
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235 if (p->strand) p->pos = bwt_sa(bwt, p->pos);
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236 }
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237 }
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238 bwt_destroy(bwt);
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239 // load reverse BWT and SA
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240 strcpy(str, prefix); strcat(str, ".rbwt"); bwt = bwt_restore_bwt(str);
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241 strcpy(str, prefix); strcat(str, ".rsa"); bwt_restore_sa(str, bwt);
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242 for (i = 0; i != n_seqs; ++i) {
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243 if (!seqs[i].strand) bwa_cal_pac_pos_core(0, bwt, 1, &seqs[i], max_mm, fnr);
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244 for (j = 0; j < seqs[i].n_multi; ++j) {
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245 bwt_multi1_t *p = seqs[i].multi + j;
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246 if (!p->strand) p->pos = bwt->seq_len - (bwt_sa(bwt, p->pos) + seqs[i].len);
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247 }
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248 }
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249 bwt_destroy(bwt);
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250 }
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251
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252 /* is_end_correct == 1 if (*pos+len) gives the correct coordinate on
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253 * forward strand. This happens when p->pos is calculated by
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254 * bwa_cal_pac_pos(). is_end_correct==0 if (*pos) gives the correct
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255 * coordinate. This happens only for color-converted alignment. */
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256 static bwa_cigar_t *refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const ubyte_t *seq, bwtint_t *_pos,
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257 int ext, int *n_cigar, int is_end_correct)
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258 {
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259 bwa_cigar_t *cigar = 0;
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260 ubyte_t *ref_seq;
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261 int l = 0, path_len, ref_len;
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262 AlnParam ap = aln_param_bwa;
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263 path_t *path;
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264 int64_t k, __pos = *_pos > l_pac? (int64_t)((int32_t)*_pos) : *_pos;
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265
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266 ref_len = len + abs(ext);
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267 if (ext > 0) {
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268 ref_seq = (ubyte_t*)calloc(ref_len, 1);
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269 for (k = __pos; k < __pos + ref_len && k < l_pac; ++k)
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270 ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
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271 } else {
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272 int64_t x = __pos + (is_end_correct? len : ref_len);
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273 ref_seq = (ubyte_t*)calloc(ref_len, 1);
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274 for (l = 0, k = x - ref_len > 0? x - ref_len : 0; k < x && k < l_pac; ++k)
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275 ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;
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276 }
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277 path = (path_t*)calloc(l+len, sizeof(path_t));
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278
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279 aln_global_core(ref_seq, l, (ubyte_t*)seq, len, &ap, path, &path_len);
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280 cigar = bwa_aln_path2cigar(path, path_len, n_cigar);
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281
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282 if (ext < 0 && is_end_correct) { // fix coordinate for reads mapped on the forward strand
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283 for (l = k = 0; k < *n_cigar; ++k) {
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284 if (__cigar_op(cigar[k]) == FROM_D) l -= __cigar_len(cigar[k]);
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285 else if (__cigar_op(cigar[k]) == FROM_I) l += __cigar_len(cigar[k]);
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286 }
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287 __pos += l;
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288 }
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289
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290 if (__cigar_op(cigar[0]) == FROM_D) { // deletion at the 5'-end
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291 __pos += __cigar_len(cigar[0]);
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292 for (k = 0; k < *n_cigar - 1; ++k) cigar[k] = cigar[k+1];
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293 --(*n_cigar);
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294 }
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295 if (__cigar_op(cigar[*n_cigar-1]) == FROM_D) --(*n_cigar); // deletion at the 3'-end
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296
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297 // change "I" at either end of the read to S. just in case. This should rarely happen...
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298 if (__cigar_op(cigar[*n_cigar-1]) == FROM_I) cigar[*n_cigar-1] = __cigar_create(3, (__cigar_len(cigar[*n_cigar-1])));
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299 if (__cigar_op(cigar[0]) == FROM_I) cigar[0] = __cigar_create(3, (__cigar_len(cigar[0])));
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300
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301 *_pos = (bwtint_t)__pos;
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302 free(ref_seq); free(path);
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303 return cigar;
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304 }
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305
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306 char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq,
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307 bwtint_t l_pac, ubyte_t *pacseq, kstring_t *str, int *_nm)
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308 {
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309 bwtint_t x, y;
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310 int z, u, c, nm = 0;
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311 str->l = 0; // reset
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312 x = pos; y = 0;
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313 if (cigar) {
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314 int k, l;
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315 for (k = u = 0; k < n_cigar; ++k) {
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316 l = __cigar_len(cigar[k]);
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317 if (__cigar_op(cigar[k]) == FROM_M) {
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318 for (z = 0; z < l && x+z < l_pac; ++z) {
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319 c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
|
|
|
320 if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
|
|
|
321 ksprintf(str, "%d", u);
|
|
|
322 kputc("ACGTN"[c], str);
|
|
|
323 ++nm;
|
|
|
324 u = 0;
|
|
|
325 } else ++u;
|
|
|
326 }
|
|
|
327 x += l; y += l;
|
|
|
328 /* } else if (cigar[k]>>14 == FROM_I || cigar[k]>>14 == 3) { */
|
|
|
329 } else if (__cigar_op(cigar[k]) == FROM_I || __cigar_op(cigar[k]) == FROM_S) {
|
|
|
330 y += l;
|
|
|
331 if (__cigar_op(cigar[k]) == FROM_I) nm += l;
|
|
|
332 } else if (__cigar_op(cigar[k]) == FROM_D) {
|
|
|
333 ksprintf(str, "%d", u);
|
|
|
334 kputc('^', str);
|
|
|
335 for (z = 0; z < l && x+z < l_pac; ++z)
|
|
|
336 kputc("ACGT"[pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3], str);
|
|
|
337 u = 0;
|
|
|
338 x += l; nm += l;
|
|
|
339 }
|
|
|
340 }
|
|
|
341 } else { // no gaps
|
|
|
342 for (z = u = 0; z < (bwtint_t)len; ++z) {
|
|
|
343 c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
|
|
|
344 if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
|
|
|
345 ksprintf(str, "%d", u);
|
|
|
346 kputc("ACGTN"[c], str);
|
|
|
347 ++nm;
|
|
|
348 u = 0;
|
|
|
349 } else ++u;
|
|
|
350 }
|
|
|
351 }
|
|
|
352 ksprintf(str, "%d", u);
|
|
|
353 *_nm = nm;
|
|
|
354 return strdup(str->s);
|
|
|
355 }
|
|
|
356
|
|
|
357 void bwa_correct_trimmed(bwa_seq_t *s)
|
|
|
358 {
|
|
|
359 if (s->len == s->full_len) return;
|
|
|
360 if (s->strand == 0) { // forward
|
|
|
361 if (s->cigar && __cigar_op(s->cigar[s->n_cigar-1]) == FROM_S) { // the last is S
|
|
|
362 s->cigar[s->n_cigar-1] += s->full_len - s->len;
|
|
|
363 } else {
|
|
|
364 if (s->cigar == 0) {
|
|
|
365 s->n_cigar = 2;
|
|
|
366 s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
|
|
|
367 s->cigar[0] = __cigar_create(0, s->len);
|
|
|
368 } else {
|
|
|
369 ++s->n_cigar;
|
|
|
370 s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
|
|
|
371 }
|
|
|
372 s->cigar[s->n_cigar-1] = __cigar_create(3, (s->full_len - s->len));
|
|
|
373 }
|
|
|
374 } else { // reverse
|
|
|
375 if (s->cigar && __cigar_op(s->cigar[0]) == FROM_S) { // the first is S
|
|
|
376 s->cigar[0] += s->full_len - s->len;
|
|
|
377 } else {
|
|
|
378 if (s->cigar == 0) {
|
|
|
379 s->n_cigar = 2;
|
|
|
380 s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
|
|
|
381 s->cigar[1] = __cigar_create(0, s->len);
|
|
|
382 } else {
|
|
|
383 ++s->n_cigar;
|
|
|
384 s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
|
|
|
385 memmove(s->cigar + 1, s->cigar, (s->n_cigar-1) * sizeof(bwa_cigar_t));
|
|
|
386 }
|
|
|
387 s->cigar[0] = __cigar_create(3, (s->full_len - s->len));
|
|
|
388 }
|
|
|
389 }
|
|
|
390 s->len = s->full_len;
|
|
|
391 }
|
|
|
392
|
|
|
393 void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns)
|
|
|
394 {
|
|
|
395 ubyte_t *pacseq, *ntpac = 0;
|
|
|
396 int i, j;
|
|
|
397 kstring_t *str;
|
|
|
398
|
|
|
399 if (ntbns) { // in color space
|
|
|
400 ntpac = (ubyte_t*)calloc(ntbns->l_pac/4+1, 1);
|
|
|
401 rewind(ntbns->fp_pac);
|
|
|
402 fread(ntpac, 1, ntbns->l_pac/4 + 1, ntbns->fp_pac);
|
|
|
403 }
|
|
|
404
|
|
|
405 if (!_pacseq) {
|
|
|
406 pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
|
|
|
407 rewind(bns->fp_pac);
|
|
|
408 fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
|
|
|
409 } else pacseq = _pacseq;
|
|
|
410 for (i = 0; i != n_seqs; ++i) {
|
|
|
411 bwa_seq_t *s = seqs + i;
|
|
|
412 for (j = 0; j < s->n_multi; ++j) {
|
|
|
413 bwt_multi1_t *q = s->multi + j;
|
|
|
414 int n_cigar;
|
|
|
415 if (q->gap == 0) continue;
|
|
|
416 q->cigar = refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, &q->pos,
|
|
|
417 (q->strand? 1 : -1) * q->gap, &n_cigar, 1);
|
|
|
418 q->n_cigar = n_cigar;
|
|
|
419 }
|
|
|
420 if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
|
|
|
421 s->cigar = refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, &s->pos,
|
|
|
422 (s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 1);
|
|
|
423 }
|
|
|
424
|
|
|
425 if (ntbns) { // in color space
|
|
|
426 for (i = 0; i < n_seqs; ++i) {
|
|
|
427 bwa_seq_t *s = seqs + i;
|
|
|
428 bwa_cs2nt_core(s, bns->l_pac, ntpac);
|
|
|
429 for (j = 0; j < s->n_multi; ++j) {
|
|
|
430 bwt_multi1_t *q = s->multi + j;
|
|
|
431 int n_cigar;
|
|
|
432 if (q->gap == 0) continue;
|
|
|
433 free(q->cigar);
|
|
|
434 q->cigar = refine_gapped_core(bns->l_pac, ntpac, s->len, q->strand? s->rseq : s->seq, &q->pos,
|
|
|
435 (q->strand? 1 : -1) * q->gap, &n_cigar, 0);
|
|
|
436 q->n_cigar = n_cigar;
|
|
|
437 }
|
|
|
438 if (s->type != BWA_TYPE_NO_MATCH && s->cigar) { // update cigar again
|
|
|
439 free(s->cigar);
|
|
|
440 s->cigar = refine_gapped_core(bns->l_pac, ntpac, s->len, s->strand? s->rseq : s->seq, &s->pos,
|
|
|
441 (s->strand? 1 : -1) * (s->n_gapo + s->n_gape), &s->n_cigar, 0);
|
|
|
442 }
|
|
|
443 }
|
|
|
444 }
|
|
|
445
|
|
|
446 // generate MD tag
|
|
|
447 str = (kstring_t*)calloc(1, sizeof(kstring_t));
|
|
|
448 for (i = 0; i != n_seqs; ++i) {
|
|
|
449 bwa_seq_t *s = seqs + i;
|
|
|
450 if (s->type != BWA_TYPE_NO_MATCH) {
|
|
|
451 int nm;
|
|
|
452 s->md = bwa_cal_md1(s->n_cigar, s->cigar, s->len, s->pos, s->strand? s->rseq : s->seq,
|
|
|
453 bns->l_pac, ntbns? ntpac : pacseq, str, &nm);
|
|
|
454 s->nm = nm;
|
|
|
455 }
|
|
|
456 }
|
|
|
457 free(str->s); free(str);
|
|
|
458
|
|
|
459 // correct for trimmed reads
|
|
|
460 if (!ntbns) // trimming is only enabled for Illumina reads
|
|
|
461 for (i = 0; i < n_seqs; ++i) bwa_correct_trimmed(seqs + i);
|
|
|
462
|
|
|
463 if (!_pacseq) free(pacseq);
|
|
|
464 free(ntpac);
|
|
|
465 }
|
|
|
466
|
|
|
467 int64_t pos_end(const bwa_seq_t *p)
|
|
|
468 {
|
|
|
469 if (p->cigar) {
|
|
|
470 int j;
|
|
|
471 int64_t x = p->pos;
|
|
|
472 for (j = 0; j != p->n_cigar; ++j) {
|
|
|
473 int op = __cigar_op(p->cigar[j]);
|
|
|
474 if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
|
|
|
475 }
|
|
|
476 return x;
|
|
|
477 } else return p->pos + p->len;
|
|
|
478 }
|
|
|
479
|
|
|
480 int64_t pos_end_multi(const bwt_multi1_t *p, int len) // analogy to pos_end()
|
|
|
481 {
|
|
|
482 if (p->cigar) {
|
|
|
483 int j;
|
|
|
484 int64_t x = p->pos;
|
|
|
485 for (j = 0; j != p->n_cigar; ++j) {
|
|
|
486 int op = __cigar_op(p->cigar[j]);
|
|
|
487 if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
|
|
|
488 }
|
|
|
489 return x;
|
|
|
490 } else return p->pos + len;
|
|
|
491 }
|
|
|
492
|
|
|
493 static int64_t pos_5(const bwa_seq_t *p)
|
|
|
494 {
|
|
|
495 if (p->type != BWA_TYPE_NO_MATCH)
|
|
|
496 return p->strand? pos_end(p) : p->pos;
|
|
|
497 return -1;
|
|
|
498 }
|
|
|
499
|
|
|
500 /* Prints <bases>\t<quals> of the sequence *p into STDOUT;
|
|
|
501 */
|
|
|
502 void bwa_print_seq_and_qual(bwa_seq_t *p) {
|
|
|
503 int j;
|
|
|
504 ubyte_t * char_ptr;
|
|
|
505
|
|
|
506 if (p->strand == 0)
|
|
|
507 for (j = 0; j != p->full_len; ++j) putchar("ACGTN"[(int)p->seq[j]]);
|
|
|
508 else for (j = 0; j != p->full_len; ++j) putchar("TGCAN"[p->seq[p->full_len - 1 - j]]);
|
|
|
509 putchar('\t');
|
|
|
510 if (p->qual) {
|
|
|
511 if (p->strand) {
|
|
|
512 // seq_reverse(p->len, p->qual, 0); // reverse quality
|
|
|
513 for ( char_ptr = p->qual + p->len - 1 ; char_ptr >= p->qual ; char_ptr-- ) putchar( *char_ptr );
|
|
|
514 } else {
|
|
|
515 printf("%s", p->qual);
|
|
|
516 }
|
|
|
517 } else printf("*");
|
|
|
518
|
|
|
519 }
|
|
|
520
|
|
|
521
|
|
|
522
|
|
|
523 void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
|
|
|
524 {
|
|
|
525 int j;
|
|
|
526 if (p->type != BWA_TYPE_NO_MATCH || (mate && mate->type != BWA_TYPE_NO_MATCH)) {
|
|
|
527 int seqid, nn, am = 0, flag = p->extra_flag;
|
|
|
528 char XT;
|
|
|
529
|
|
|
530 if (p->type == BWA_TYPE_NO_MATCH) {
|
|
|
531 p->pos = mate->pos;
|
|
|
532 p->strand = mate->strand;
|
|
|
533 flag |= SAM_FSU;
|
|
|
534 j = 1;
|
|
|
535 } else j = pos_end(p) - p->pos; // j is the length of the reference in the alignment
|
|
|
536
|
|
|
537 // get seqid
|
|
|
538 nn = bns_coor_pac2real(bns, p->pos, j, &seqid);
|
|
|
539 if (p->type != BWA_TYPE_NO_MATCH && p->pos + j - bns->anns[seqid].offset > bns->anns[seqid].len)
|
|
|
540 flag |= SAM_FSU; // flag UNMAP as this alignment bridges two adjacent reference sequences
|
|
|
541
|
|
|
542 // update flag and print it
|
|
|
543 if (p->strand) flag |= SAM_FSR;
|
|
|
544 if (mate) {
|
|
|
545 if (mate->type != BWA_TYPE_NO_MATCH) {
|
|
|
546 if (mate->strand) flag |= SAM_FMR;
|
|
|
547 } else flag |= SAM_FMU;
|
|
|
548 }
|
|
|
549 printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
|
|
|
550 printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
|
|
|
551
|
|
|
552 // print CIGAR
|
|
|
553 if (p->cigar) {
|
|
|
554 for (j = 0; j != p->n_cigar; ++j)
|
|
|
555 printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
|
|
|
556 } else if (p->type == BWA_TYPE_NO_MATCH) printf("*");
|
|
|
557 else printf("%dM", p->len);
|
|
|
558
|
|
|
559 // print mate coordinate
|
|
|
560 if (mate && mate->type != BWA_TYPE_NO_MATCH) {
|
|
|
561 int m_seqid, m_is_N;
|
|
|
562 long long isize;
|
|
|
563 am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
|
|
|
564 // redundant calculation here, but should not matter too much
|
|
|
565 m_is_N = bns_coor_pac2real(bns, mate->pos, mate->len, &m_seqid);
|
|
|
566 printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
|
|
|
567 isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
|
|
|
568 if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
|
|
|
569 printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
|
|
|
570 } else if (mate) printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
|
|
|
571 else printf("\t*\t0\t0\t");
|
|
|
572
|
|
|
573 // print sequence and quality
|
|
|
574 bwa_print_seq_and_qual(p);
|
|
|
575
|
|
|
576 if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
|
|
|
577 if (p->type != BWA_TYPE_NO_MATCH) {
|
|
|
578 int i;
|
|
|
579 // calculate XT tag
|
|
|
580 XT = "NURM"[p->type];
|
|
|
581 if (nn > 10) XT = 'N';
|
|
|
582 // print tags
|
|
|
583 printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
|
|
|
584 if (nn) printf("\tXN:i:%d", nn);
|
|
|
585 if (mate) printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
|
|
|
586 if (p->type != BWA_TYPE_MATESW) { // X0 and X1 are not available for this type of alignment
|
|
|
587 printf("\tX0:i:%d", p->c1);
|
|
|
588 if (p->c1 <= max_top2) printf("\tX1:i:%d", p->c2);
|
|
|
589 }
|
|
|
590 printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
|
|
|
591 if (p->md) printf("\tMD:Z:%s", p->md);
|
|
|
592 // print multiple hits
|
|
|
593 if (p->n_multi) {
|
|
|
594 printf("\tXA:Z:");
|
|
|
595 for (i = 0; i < p->n_multi; ++i) {
|
|
|
596 bwt_multi1_t *q = p->multi + i;
|
|
|
597 int k;
|
|
|
598 j = pos_end_multi(q, p->len) - q->pos;
|
|
|
599 nn = bns_coor_pac2real(bns, q->pos, j, &seqid);
|
|
|
600 printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
|
|
|
601 (int)(q->pos - bns->anns[seqid].offset + 1));
|
|
|
602 if (q->cigar) {
|
|
|
603 for (k = 0; k < q->n_cigar; ++k)
|
|
|
604 printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
|
|
|
605 } else printf("%dM", p->len);
|
|
|
606 printf(",%d;", q->gap + q->mm);
|
|
|
607 }
|
|
|
608 }
|
|
|
609 }
|
|
|
610 putchar('\n');
|
|
|
611 } else { // this read has no match
|
|
|
612 ubyte_t *s = p->strand? p->rseq : p->seq;
|
|
|
613 int flag = p->extra_flag | SAM_FSU;
|
|
|
614 if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
|
|
|
615 printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
|
|
|
616 for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
|
|
|
617 putchar('\t');
|
|
|
618 if (p->qual) {
|
|
|
619 if (p->strand) {
|
|
|
620 // seq_reverse(p->len, p->qual, 0); // reverse quality
|
|
|
621 for ( s = p->qual + p->len - 1 ; s >= p->qual ; s-- ) putchar( *s );
|
|
|
622
|
|
|
623 } else {
|
|
|
624 printf("%s", p->qual);
|
|
|
625 }
|
|
|
626 } else printf("*");
|
|
|
627 if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
|
|
|
628 putchar('\n');
|
|
|
629 }
|
|
|
630 }
|
|
|
631
|
|
|
632 /* UNUSED
|
|
|
633 void bwa_print_partial_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
|
|
|
634 {
|
|
|
635 int j;
|
|
|
636 if (p->type != BWA_TYPE_NO_MATCH || (mate && mate->type != BWA_TYPE_NO_MATCH)) {
|
|
|
637 int seqid, nn, am = 0, flag = p->extra_flag;
|
|
|
638 char XT;
|
|
|
639
|
|
|
640 if (p->type == BWA_TYPE_NO_MATCH) {
|
|
|
641 p->pos = mate->pos;
|
|
|
642 p->strand = mate->strand;
|
|
|
643 flag |= SAM_FSU;
|
|
|
644 j = 1;
|
|
|
645 } else j = pos_end(p) - p->pos; // j is the length of the reference in the alignment
|
|
|
646
|
|
|
647 // get seqid
|
|
|
648 nn = bns_coor_pac2real(bns, p->pos, j, &seqid);
|
|
|
649 if (p->type != BWA_TYPE_NO_MATCH && p->pos + j - bns->anns[seqid].offset > bns->anns[seqid].len)
|
|
|
650 flag |= SAM_FSU; // flag UNMAP as this alignment bridges two adjacent reference sequences
|
|
|
651
|
|
|
652 // update flag and print it
|
|
|
653 if (p->strand) flag |= SAM_FSR;
|
|
|
654 if (mate) {
|
|
|
655 if (mate->type != BWA_TYPE_NO_MATCH) {
|
|
|
656 if (mate->strand) flag |= SAM_FMR;
|
|
|
657 } else flag |= SAM_FMU;
|
|
|
658 }
|
|
|
659 printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
|
|
|
660 printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);
|
|
|
661
|
|
|
662 // print CIGAR
|
|
|
663 if (p->cigar) {
|
|
|
664 for (j = 0; j != p->n_cigar; ++j)
|
|
|
665 printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
|
|
|
666 } else if (p->type == BWA_TYPE_NO_MATCH) printf("*");
|
|
|
667 else printf("%dM", p->len);
|
|
|
668
|
|
|
669 // print mate coordinate
|
|
|
670 if (mate && mate->type != BWA_TYPE_NO_MATCH) {
|
|
|
671 int m_seqid, m_is_N;
|
|
|
672 long long isize;
|
|
|
673 am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
|
|
|
674 // redundant calculation here, but should not matter too much
|
|
|
675 m_is_N = bns_coor_pac2real(bns, mate->pos, mate->len, &m_seqid);
|
|
|
676 printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
|
|
|
677 isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
|
|
|
678 if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
|
|
|
679 printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
|
|
|
680 } else if (mate) printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
|
|
|
681 else printf("\t*\t0\t0\t");
|
|
|
682
|
|
|
683
|
|
|
684 if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
|
|
|
685 if (p->type != BWA_TYPE_NO_MATCH) {
|
|
|
686 int i;
|
|
|
687 // calculate XT tag
|
|
|
688 XT = "NURM"[p->type];
|
|
|
689 if (nn > 10) XT = 'N';
|
|
|
690 // print tags
|
|
|
691 printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
|
|
|
692 if (nn) printf("\tXN:i:%d", nn);
|
|
|
693 if (mate) printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
|
|
|
694 printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
|
|
|
695 if (p->md) printf("\tMD:Z:%s", p->md);
|
|
|
696 }
|
|
|
697 putchar('\n');
|
|
|
698 } else { // this read has no match
|
|
|
699 ubyte_t *s = p->strand? p->rseq : p->seq;
|
|
|
700 int flag = p->extra_flag | SAM_FSU;
|
|
|
701 if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
|
|
|
702 printf("%d\t*\t0\t0\t*\t*\t0\t0\t", flag);
|
|
|
703 if (p->clip_len < p->full_len) printf("\tXC:i:%d", p->clip_len);
|
|
|
704 putchar('\n');
|
|
|
705 }
|
|
|
706 }
|
|
|
707
|
|
|
708 */
|
|
|
709
|
|
|
710 bntseq_t *bwa_open_nt(const char *prefix)
|
|
|
711 {
|
|
|
712 bntseq_t *ntbns;
|
|
|
713 char *str;
|
|
|
714 str = (char*)calloc(strlen(prefix) + 10, 1);
|
|
|
715 strcat(strcpy(str, prefix), ".nt");
|
|
|
716 ntbns = bns_restore(str);
|
|
|
717 free(str);
|
|
|
718 return ntbns;
|
|
|
719 }
|
|
|
720
|
|
|
721 void bwa_print_sam_SQ(const bntseq_t *bns)
|
|
|
722 {
|
|
|
723 int i;
|
|
|
724 for (i = 0; i < bns->n_seqs; ++i)
|
|
|
725 printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
|
|
|
726 }
|
|
|
727
|
|
|
728 void bwase_initialize()
|
|
|
729 {
|
|
|
730 int i;
|
|
|
731 for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
|
|
|
732 }
|
|
|
733
|
|
|
734 void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ)
|
|
|
735 {
|
|
|
736 int i, n_seqs, tot_seqs = 0, m_aln;
|
|
|
737 bwt_aln1_t *aln = 0;
|
|
|
738 bwa_seq_t *seqs;
|
|
|
739 bwa_seqio_t *ks;
|
|
|
740 clock_t t;
|
|
|
741 bntseq_t *bns, *ntbns = 0;
|
|
|
742 FILE *fp_sa;
|
|
|
743 gap_opt_t opt;
|
|
|
744
|
|
|
745 // initialization
|
|
|
746 bwase_initialize();
|
|
|
747 bns = bns_restore(prefix);
|
|
|
748 srand48(bns->seed);
|
|
|
749 ks = bwa_seq_open(fn_fa);
|
|
|
750 fp_sa = xopen(fn_sa, "r");
|
|
|
751
|
|
|
752 // core loop
|
|
|
753 m_aln = 0;
|
|
|
754 fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
|
|
|
755 if (!(opt.mode & BWA_MODE_COMPREAD)) // in color space; initialize ntpac
|
|
|
756 ntbns = bwa_open_nt(prefix);
|
|
|
757 bwa_print_sam_SQ(bns);
|
|
|
758 while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode & BWA_MODE_COMPREAD, opt.trim_qual)) != 0) {
|
|
|
759 tot_seqs += n_seqs;
|
|
|
760 t = clock();
|
|
|
761
|
|
|
762 // read alignment
|
|
|
763 for (i = 0; i < n_seqs; ++i) {
|
|
|
764 bwa_seq_t *p = seqs + i;
|
|
|
765 int n_aln;
|
|
|
766 fread(&n_aln, 4, 1, fp_sa);
|
|
|
767 if (n_aln > m_aln) {
|
|
|
768 m_aln = n_aln;
|
|
|
769 aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln);
|
|
|
770 }
|
|
|
771 fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
|
|
|
772 bwa_aln2seq_core(n_aln, aln, p, 1, n_occ);
|
|
|
773 // seq_reverse(p->len, p->seq, 0);
|
|
|
774 }
|
|
|
775
|
|
|
776 fprintf(stderr, "[bwa_aln_core] convert to sequence coordinate... ");
|
|
|
777 bwa_cal_pac_pos(prefix, n_seqs, seqs, opt.max_diff, opt.fnr); // forward bwt will be destroyed here
|
|
|
778 fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
|
|
|
779
|
|
|
780 for (i = 0; i < n_seqs; ++i) {
|
|
|
781 bwa_seq_t *p = seqs + i;
|
|
|
782 seq_reverse(p->len, p->seq, 0);
|
|
|
783 }
|
|
|
784
|
|
|
785 fprintf(stderr, "[bwa_aln_core] refine gapped alignments... ");
|
|
|
786 bwa_refine_gapped(bns, n_seqs, seqs, 0, ntbns);
|
|
|
787 fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
|
|
|
788
|
|
|
789 fprintf(stderr, "[bwa_aln_core] print alignments... ");
|
|
|
790 for (i = 0; i < n_seqs; ++i)
|
|
|
791 bwa_print_sam1(bns, seqs + i, 0, opt.mode, opt.max_top2);
|
|
|
792 fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
|
|
|
793
|
|
|
794 bwa_free_read_seq(n_seqs, seqs);
|
|
|
795 fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
|
|
|
796 }
|
|
|
797
|
|
|
798 // destroy
|
|
|
799 bwa_seq_close(ks);
|
|
|
800 if (ntbns) bns_destroy(ntbns);
|
|
|
801 bns_destroy(bns);
|
|
|
802 fclose(fp_sa);
|
|
|
803 free(aln);
|
|
|
804 }
|
|
|
805
|
|
|
806 void bwa_print_all_hits(const char *prefix, const char *fn_sa, const char *fn_fa, int max_extra_occ)
|
|
|
807 {
|
|
|
808 int i, n_seqs, tot_seqs = 0, m_aln, m_rest;
|
|
|
809 bwt_aln1_t *aln = 0;
|
|
|
810 bwa_seq_t *seqs;
|
|
|
811 bwa_seqio_t *ks;
|
|
|
812 clock_t t,t_convert, t_refine, t_write;;
|
|
|
813 bntseq_t *bns, *ntbns = 0;
|
|
|
814 FILE *fp_sa;
|
|
|
815 gap_opt_t opt;
|
|
|
816
|
|
|
817 //****** below modified (added) for multiple hit printout:
|
|
|
818
|
|
|
819 bwa_seq_t * rest_seqs = 0; // this array will keep (shallow) replicas of the current sequence;
|
|
|
820 // each of the replicas will be updated with its own alignment
|
|
|
821 // selected from all the (multiple) alignmens available for the current seq.
|
|
|
822
|
|
|
823 bwt_t *bwt[2];
|
|
|
824 char str[1024];
|
|
|
825 ubyte_t *pacseq;
|
|
|
826
|
|
|
827 t = clock();
|
|
|
828 fprintf(stderr, "[bwa_aln_core] Data structures initialized: ");
|
|
|
829
|
|
|
830
|
|
|
831 strcpy(str, prefix); strcat(str, ".bwt"); bwt[0] = bwt_restore_bwt(str);
|
|
|
832 strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt[0]);
|
|
|
833
|
|
|
834 // load reverse BWT and SA
|
|
|
835 strcpy(str, prefix); strcat(str, ".rbwt"); bwt[1] = bwt_restore_bwt(str);
|
|
|
836 strcpy(str, prefix); strcat(str, ".rsa"); bwt_restore_sa(str, bwt[1]);
|
|
|
837 //***************
|
|
|
838
|
|
|
839 // initialization
|
|
|
840 bwase_initialize();
|
|
|
841 bns = bns_restore(prefix);
|
|
|
842 srand48(bns->seed);
|
|
|
843 ks = bwa_seq_open(fn_fa);
|
|
|
844 fp_sa = xopen(fn_sa, "r");
|
|
|
845
|
|
|
846 pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
|
|
|
847 rewind(bns->fp_pac);
|
|
|
848 fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
|
|
|
849
|
|
|
850
|
|
|
851 // core loop
|
|
|
852 m_aln = 0;
|
|
|
853 m_rest = 0;
|
|
|
854
|
|
|
855 fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
|
|
|
856 if (!(opt.mode & BWA_MODE_COMPREAD)) // in color space; initialize ntpac
|
|
|
857 ntbns = bwa_open_nt(prefix);
|
|
|
858 bwa_print_sam_SQ(bns);
|
|
|
859
|
|
|
860 fprintf(stderr, "%.2f sec\n", (float)(clock()-t) / CLOCKS_PER_SEC);
|
|
|
861
|
|
|
862 t = clock();
|
|
|
863
|
|
|
864 max_extra_occ++; // now this variable holds TOTAL number of alignments we want to print (1+requested extra).
|
|
|
865
|
|
|
866 while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode & BWA_MODE_COMPREAD, opt.trim_qual)) != 0) {
|
|
|
867 tot_seqs += n_seqs;
|
|
|
868 t_convert = 0;
|
|
|
869 t_refine = 0;
|
|
|
870 t_write = 0;
|
|
|
871
|
|
|
872 fprintf(stderr, "[bwa_aln_core] %d sequences loaded: ",n_seqs);
|
|
|
873 fprintf(stderr, "%.2f sec\n", (float)(clock()-t) / CLOCKS_PER_SEC);
|
|
|
874
|
|
|
875
|
|
|
876 // read alignment
|
|
|
877 for (i = 0; i < n_seqs; ++i) {
|
|
|
878
|
|
|
879 bwa_seq_t *p = seqs + i;
|
|
|
880 int n_aln, n_occ, k, rest;
|
|
|
881 fread(&n_aln, 4, 1, fp_sa);
|
|
|
882 if (n_aln > m_aln) {
|
|
|
883 m_aln = n_aln;
|
|
|
884 aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln);
|
|
|
885 }
|
|
|
886
|
|
|
887 fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
|
|
|
888 for ( k = n_occ = 0 ; k < n_aln; ++k ) {
|
|
|
889 const bwt_aln1_t *q = aln + k;
|
|
|
890 n_occ += q->l - q->k + 1;
|
|
|
891 } /* n_occ is now keeping total number of available alignments to the reference
|
|
|
892 (i.e. placements, NOT bwa records, each of which can describe few placements)
|
|
|
893 */
|
|
|
894
|
|
|
895 // we are going to keep and print 'rest' alignments:
|
|
|
896 rest = ((n_occ > max_extra_occ)? max_extra_occ : n_occ);
|
|
|
897
|
|
|
898 if ( rest == 0 ) rest++; /* we need at least one record, even if it is going to say "UNMAPPED" */
|
|
|
899
|
|
|
900 if ( rest > m_rest ) {
|
|
|
901 // reallocate rest_seqs array (only if needed) to ensure it can keep 'rest' records
|
|
|
902 m_rest = rest;
|
|
|
903 rest_seqs = (bwa_seq_t*)realloc(rest_seqs,sizeof(bwa_seq_t)*m_rest);
|
|
|
904 }
|
|
|
905 // initialize 'rest' replicas of the current sequence record
|
|
|
906 for ( k = 0 ; k < rest ; k++ ) {
|
|
|
907 rest_seqs[k] = *p; /* clone current sequence p; IMPORTANT: it's a shallow copy */
|
|
|
908 }
|
|
|
909
|
|
|
910 bwa_aln2seq_all(n_aln, aln, rest,rest_seqs);
|
|
|
911 // now each of the replicas carries its own bwa alignment selected from all alignments
|
|
|
912 // available for the current sequence *p.
|
|
|
913
|
|
|
914 /* compute positions of the alignments on the ref: */
|
|
|
915 t = clock();
|
|
|
916
|
|
|
917 bwa_cal_pac_pos_core(bwt[0],bwt[1], rest, rest_seqs, opt.max_diff, opt.fnr );
|
|
|
918 t_convert += ( clock() - t );
|
|
|
919 *p = rest_seqs[0]; // copy first selected alignment back into p;
|
|
|
920
|
|
|
921 seq_reverse(p->len, p->seq,0);
|
|
|
922
|
|
|
923 /* compute positions of the alignments on the ref: */
|
|
|
924 t = clock();
|
|
|
925
|
|
|
926 bwa_cal_pac_pos_core(bwt[0],bwt[1], rest, rest_seqs, opt.max_diff, opt.fnr );
|
|
|
927 t_convert += ( clock() - t );
|
|
|
928
|
|
|
929 t = clock();
|
|
|
930
|
|
|
931 bwa_refine_gapped(bns,rest,rest_seqs,pacseq,ntbns); // refine all gapped aligns in our replicas;
|
|
|
932 // side effect: cigars will be allocated for each replica
|
|
|
933 t_refine += ( clock() - t );
|
|
|
934
|
|
|
935 t = clock();
|
|
|
936 // for ( k = 0 ; k < n_seqs ; k++ ) {
|
|
|
937 for ( k = 0 ; k < rest ; k++ ) {
|
|
|
938
|
|
|
939 bwa_print_sam1(bns, rest_seqs + k, 0, opt.mode, opt.max_top2);
|
|
|
940 // cigar was allocated for us in every replica as a side effect, free it now:
|
|
|
941 free ( (rest_seqs+k)->cigar );
|
|
|
942 }
|
|
|
943 t_write+= ( clock()-t);
|
|
|
944
|
|
|
945 }
|
|
|
946
|
|
|
947 bwa_free_read_seq(n_seqs, seqs);
|
|
|
948
|
|
|
949 fprintf(stderr, "[bwa_aln_core] convert %d sequences to sequence coordinate: ",n_seqs);
|
|
|
950 fprintf(stderr, "%.2f sec\n", (float)t_convert / CLOCKS_PER_SEC);
|
|
|
951 fprintf(stderr, "[bwa_aln_core] refine gapped alignments for %d sequences: ", n_seqs);
|
|
|
952 fprintf(stderr, "%.2f sec\n", (float)t_refine / CLOCKS_PER_SEC);
|
|
|
953 fprintf(stderr, "[bwa_aln_core] print alignments for %d sequences: ", n_seqs);
|
|
|
954 fprintf(stderr, "%.2f sec\n", (float)t_write/ CLOCKS_PER_SEC);
|
|
|
955 fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
|
|
|
956
|
|
|
957 t = clock();
|
|
|
958 }
|
|
|
959
|
|
|
960 // destroy
|
|
|
961 bwt_destroy(bwt[0]);
|
|
|
962 bwt_destroy(bwt[1]);
|
|
|
963
|
|
|
964 free(rest_seqs);
|
|
|
965 free(pacseq);
|
|
|
966
|
|
|
967 bwa_seq_close(ks);
|
|
|
968 if (ntbns) bns_destroy(ntbns);
|
|
|
969 bns_destroy(bns);
|
|
|
970 fclose(fp_sa);
|
|
|
971 free(aln);
|
|
|
972 }
|
|
|
973
|
|
|
974 int bwa_sai2sam_se(int argc, char *argv[])
|
|
|
975 {
|
|
|
976 int c, n_occ = 3;
|
|
|
977 int do_full_sam = 0;
|
|
|
978 while ((c = getopt(argc, argv, "hsn:f:")) >= 0) {
|
|
|
979 switch (c) {
|
|
|
980 case 'h': break;
|
|
|
981 case 's': do_full_sam = 1; break;
|
|
|
982 case 'n': n_occ = atoi(optarg); break;
|
|
|
983 case 'f': freopen(optarg, "w", stdout); break;
|
|
|
984 default: return 1;
|
|
|
985 }
|
|
|
986 }
|
|
|
987
|
|
|
988 if (optind + 3 > argc) {
|
|
|
989 fprintf(stderr, "Usage: bwa samse [-n max_occ [-s] ] [-f out.sam] <prefix> <in.sai> <in.fq>\n");
|
|
|
990 return 1;
|
|
|
991 }
|
|
|
992 if ( do_full_sam ) bwa_print_all_hits(argv[optind], argv[optind+1], argv[optind+2], n_occ);
|
|
|
993 else bwa_sai2sam_se_core(argv[optind], argv[optind+1], argv[optind+2], n_occ);
|
|
|
994 return 0;
|
|
|
995 }
|
